diff --git a/src/commands/archive-setup/archive.setup.ts b/src/commands/archive-setup/archive.setup.ts
index a9c5b965..396a7851 100644
--- a/src/commands/archive-setup/archive.setup.ts
+++ b/src/commands/archive-setup/archive.setup.ts
@@ -36,7 +36,7 @@ export const archiveSetup = command({
     const archiveLocation = getArchiveLocation(args.path, archiveBucketName);
     const saveArchiveLocationTo = new URL('archive-location', args.output);
 
-    await fsa.write(saveArchiveLocationTo, protocolAwareString(archiveLocation));
+    await fsa.write(saveArchiveLocationTo, protocolAwareString(archiveLocation, true));
 
     logger.info(
       { duration: performance.now() - startTime, archiveLocation: protocolAwareString(archiveLocation) },
diff --git a/src/commands/copy/copy.ts b/src/commands/copy/copy.ts
index 616801ce..9433f417 100644
--- a/src/commands/copy/copy.ts
+++ b/src/commands/copy/copy.ts
@@ -14,8 +14,8 @@ import { mergeStats } from './copy-helpers.ts';
 import type { CopyContract, CopyStats } from './copy-rpc.ts';
 
 const CopyValidator = z.object({
-  source: z.string().transform((val) => protocolAwareString(fsa.toUrl(val))),
-  target: z.string().transform((val) => protocolAwareString(fsa.toUrl(val))),
+  source: z.string().transform((val) => protocolAwareString(fsa.toUrl(val), true)),
+  target: z.string().transform((val) => protocolAwareString(fsa.toUrl(val), true)),
 });
 const CopyManifest = z.array(CopyValidator);
 
diff --git a/src/commands/create-manifest/create-manifest.ts b/src/commands/create-manifest/create-manifest.ts
index 29b91da3..50915be0 100644
--- a/src/commands/create-manifest/create-manifest.ts
+++ b/src/commands/create-manifest/create-manifest.ts
@@ -65,7 +65,7 @@ export const commandCreateManifest = command({
         const targetLocation = new URL(`manifest-${targetHash}.json`, actionLocation);
         const targetAction: ActionCopy = { action: 'copy', parameters: { manifest: current } };
         await fsa.write(targetLocation, JSON.stringify(targetAction));
-        outputCopy.push(protocolAwareString(targetLocation));
+        outputCopy.push(protocolAwareString(targetLocation, true));
       } else {
         outputCopy.push(gzipSync(outBuf).toString('base64url'));
       }
diff --git a/src/commands/list/list.ts b/src/commands/list/list.ts
index 1190bc2f..68546df4 100644
--- a/src/commands/list/list.ts
+++ b/src/commands/list/list.ts
@@ -40,7 +40,7 @@ export const commandList = command({
     }
     const listLocations = args.location.flat();
     const outputFiles = await getFiles(listLocations, args);
-    const decodedFiles = outputFiles.map((outputFile) => outputFile.map((url) => protocolAwareString(url)));
+    const decodedFiles = outputFiles.map((outputFile) => outputFile.map((url) => protocolAwareString(url, true)));
     if (args.output) await fsa.write(args.output, JSON.stringify(decodedFiles));
   },
 });
diff --git a/src/commands/stac-catalog/__test__/stac.catalog.test.ts b/src/commands/stac-catalog/__test__/stac.catalog.test.ts
index aff33d98..bf797564 100644
--- a/src/commands/stac-catalog/__test__/stac.catalog.test.ts
+++ b/src/commands/stac-catalog/__test__/stac.catalog.test.ts
@@ -2,9 +2,7 @@ import assert from 'node:assert';
 import { beforeEach, describe, it } from 'node:test';
 
 import { fsa, FsMemory } from '@chunkd/fs';
-import { pathToFileURL } from 'url';
 
-import { makeRelative } from '../../../utils/filelist.ts';
 import { createLinks } from '../stac.catalog.ts';
 
 describe('stacCatalog', () => {
@@ -42,27 +40,3 @@ describe('stacCatalog', () => {
     ]);
   });
 });
-
-describe('makeRelative', () => {
-  it('should make relative urls', () => {
-    assert.equal(
-      makeRelative(fsa.toUrl('s3://linz-imagery/'), fsa.toUrl('s3://linz-imagery/catalog.json')),
-      './catalog.json',
-    );
-  });
-
-  it('should make relative from absolute paths', () => {
-    assert.equal(
-      makeRelative(pathToFileURL('/home/blacha/'), pathToFileURL('/home/blacha/catalog.json')),
-      './catalog.json',
-    );
-  });
-
-  it('should make relative relative paths', () => {
-    assert.equal(makeRelative(pathToFileURL(process.cwd() + '/'), pathToFileURL('./catalog.json')), './catalog.json');
-  });
-
-  it('should not make relative on different paths', () => {
-    assert.throws(() => makeRelative(pathToFileURL('/home/blacha/'), pathToFileURL('/home/test/catalog.json')), Error);
-  });
-});
diff --git a/src/commands/tileindex-validate/tileindex.validate.ts b/src/commands/tileindex-validate/tileindex.validate.ts
index c0d3a9d6..2e9ce4aa 100644
--- a/src/commands/tileindex-validate/tileindex.validate.ts
+++ b/src/commands/tileindex-validate/tileindex.validate.ts
@@ -347,7 +347,7 @@ async function getTiffsMetadata(tiffs: Tiff[], locations: URL[]): Promise<TiffsM
   if (roundedGsds.size > 1) {
     logger.error({ gsds: [...gsds], roundedGsds: [...roundedGsds] }, 'TileIndex:InconsistentGSDs:Failed');
     throw new Error(
-      `Inconsistent GSDs found: ${[...roundedGsds].join(', ')} ${[...gsds].join(',')}, ${locations.map(protocolAwareString).join(',')}`,
+      `Inconsistent GSDs found: ${[...roundedGsds].join(', ')} ${[...gsds].join(',')}, ${locations.map((loc) => protocolAwareString(loc)).join(',')}`,
     );
   } else if (gsds.size > 1) {
     logger.info({ gsds: [...gsds], roundedGsds: [...roundedGsds] }, 'TileIndex:InconsistentGSDs:RoundedToMatch');
diff --git a/src/utils/__test__/filelist.test.ts b/src/utils/__test__/filelist.test.ts
index c9c15cb7..5e5fb939 100644
--- a/src/utils/__test__/filelist.test.ts
+++ b/src/utils/__test__/filelist.test.ts
@@ -1,10 +1,13 @@
 import assert from 'node:assert';
 import { describe, it } from 'node:test';
+import { pathToFileURL } from 'node:url';
 
 import { fsa } from '@chunkd/fs';
 
 import type { TiffLocation } from '../../commands/tileindex-validate/tileindex.validate.ts';
 import type { FileListEntryClass } from '../filelist.ts';
+import { encodePercentSigns } from '../filelist.ts';
+import { makeRelative } from '../filelist.ts';
 import { createFileList, protocolAwareString } from '../filelist.ts';
 
 describe('createFileList', () => {
@@ -65,6 +68,12 @@ describe('URL handling with special characters', () => {
         expectedTransformed:
           's3://linz-topographic-upload/landpro/Gisborne_2023/Non_Priority_3/VECTOR/EP%23462_Gisborne_LOT_15-16-17.dgn',
       },
+      {
+        original:
+          's3://linz-hydrographic-archive/Authoritative_Surveys/HS72_Taranaki/Processed_Data/3_Processed/1_GSF_PROJECTS/HS72_Block M_GSF Project/SD/HS72_M_95%_C.I_4m_39-110m.sd',
+        expectedTransformed:
+          's3://linz-hydrographic-archive/Authoritative_Surveys/HS72_Taranaki/Processed_Data/3_Processed/1_GSF_PROJECTS/HS72_Block M_GSF Project/SD/HS72_M_95%25_C.I_4m_39-110m.sd',
+      },
       {
         original:
           's3://linz-topographic-archive/landpro/Gisborne_2023/Non_Priority_3/VECTOR/EP#462_Gisborne_LOT_15-16-17.dgn',
@@ -100,7 +109,7 @@ describe('URL handling with special characters', () => {
     for (const testCase of testCases) {
       // This is what happens in the CopyValidator
       const url1 = fsa.toUrl(testCase.original);
-      const transformedPath = protocolAwareString(url1);
+      const transformedPath = protocolAwareString(url1, true);
 
       // This is what happens in the copy worker
       const url2 = fsa.toUrl(transformedPath);
@@ -121,3 +130,70 @@ describe('URL handling with special characters', () => {
     }
   });
 });
+
+describe('makeRelative', () => {
+  it('should make relative urls', () => {
+    assert.equal(
+      makeRelative(fsa.toUrl('s3://linz-imagery/'), fsa.toUrl('s3://linz-imagery/catalog.json')),
+      './catalog.json',
+    );
+  });
+
+  it('should make relative from absolute paths', () => {
+    assert.equal(
+      makeRelative(pathToFileURL('/home/blacha/'), pathToFileURL('/home/blacha/catalog.json')),
+      './catalog.json',
+    );
+  });
+
+  it('should make relative relative paths', () => {
+    assert.equal(makeRelative(pathToFileURL(process.cwd() + '/'), pathToFileURL('./catalog.json')), './catalog.json');
+  });
+
+  it('should not make relative on different paths', () => {
+    assert.throws(() => makeRelative(pathToFileURL('/home/blacha/'), pathToFileURL('/home/test/catalog.json')), Error);
+  });
+
+  it('should handle URLs with spaces', () => {
+    const base = new URL('s3://bucket/path/');
+    const fileWithSpace = new URL('s3://bucket/path/with%20space/file.txt');
+    assert.equal(makeRelative(base, fileWithSpace), './with space/file.txt');
+  });
+
+  it('should handle URLs with special characters', () => {
+    const base = new URL('memory://bucket/path/');
+    const fileWithHash = new URL('memory://bucket/path/file%23hash.txt');
+    const fileWithBracket = new URL('memory://bucket/path/file[bracket].txt');
+    assert.equal(makeRelative(base, fileWithHash), './file#hash.txt');
+    assert.equal(makeRelative(base, fileWithBracket), './file[bracket].txt');
+  });
+
+  it('should handle file with percent sign (not followed by two hex digits)', () => {
+    const base = new URL('s3://bucket/path/');
+    const tricky = new URL('s3://bucket/path/95%_C.I_4m_40-110m.sd');
+    assert.equal(makeRelative(base, tricky), './95%_C.I_4m_40-110m.sd');
+  });
+
+  it('should throw if strict and not a subfolder', () => {
+    const base = new URL('s3://bucket/path/');
+    const outside = new URL('s3://bucket/other/file.txt');
+    assert.throws(() => makeRelative(base, outside, true));
+  });
+});
+
+describe('encodePercentSigns', () => {
+  it('should encode lone percent signs', () => {
+    assert.equal(encodePercentSigns('HS72_M_95%_C.I_4m_39-110m.sd'), 'HS72_M_95%25_C.I_4m_39-110m.sd');
+    assert.equal(encodePercentSigns('%foo%'), '%25foo%25');
+  });
+
+  it('should not encode percent signs followed by two hex digits', () => {
+    assert.equal(encodePercentSigns('foo%20bar'), 'foo%20bar');
+    assert.equal(encodePercentSigns('%41%42%43'), '%41%42%43');
+  });
+
+  it('should encode percent signs not followed by two hex digits', () => {
+    assert.equal(encodePercentSigns('foo%2Gbar'), 'foo%252Gbar');
+    assert.equal(encodePercentSigns('foo%'), 'foo%25');
+  });
+});
diff --git a/src/utils/filelist.ts b/src/utils/filelist.ts
index 23556832..5f7dafb4 100644
--- a/src/utils/filelist.ts
+++ b/src/utils/filelist.ts
@@ -10,23 +10,31 @@ export const HttpProtocols = ['https:', 'http:'];
  * For http(s):// URLs it returns the full URL (with encoded characters)
  * For other protocols it decodes the characters and
  * for file:// URL it creates a relative path from the current working directory
- * For non-HTTP URLs, # characters are kept encoded as %23 to prevent
- * them from being interpreted as URL fragments.
+ * For non-HTTP URLs, if encodeSpecialChars is true, # characters and % signs are kept encoded as %23 and %25 respectively  to prevent
+ * them from being interpreted as URL fragments or special characters.
  *
  * @param targetLocation URL to convert to string
+ * @param encodeSpecialChars whether to encode special characters (#, %) for non-HTTP URLs
  * @returns string representation of the URL
  */
-export function protocolAwareString(targetLocation: URL): string {
+export function protocolAwareString(targetLocation: URL, encodeSpecialChars = false): string {
   if (HttpProtocols.includes(targetLocation.protocol)) {
     return targetLocation.href;
   }
   if (targetLocation.protocol === 'file:') {
     return fileURLToPath(targetLocation);
   }
-
-  // Decode URI components but keep # characters encoded to prevent
-  // them from being interpreted as URL fragments
-  return decodeURIComponent(targetLocation.href).replace(/#/g, '%23');
+  if (!encodeSpecialChars) {
+    return decodeURIComponent(targetLocation.href);
+  }
+  // Encode % signs to avoid decodeURIComponent errors
+  const targetLocationWithEncodedPercents = encodePercentSigns(targetLocation.href);
+  // Decode URI components
+  const targetLocationDecodedURI = decodeURIComponent(targetLocationWithEncodedPercents);
+  // Encode % signs again to avoid issues using the decoded URI with fsa
+  // Encode # characters to prevent them from being interpreted as URL fragments
+  const targetLocationWithEncodedHashesAndPercents = encodePercentSigns(targetLocationDecodedURI).replace(/#/g, '%23');
+  return targetLocationWithEncodedHashesAndPercents;
 }
 
 /**
@@ -65,7 +73,19 @@ export function makeRelative(baseLocation: URL, fileLocation: URL, strict = true
   if (HttpProtocols.includes(fileLocation.protocol)) {
     return fileLocation.href.replace(baseLocationFolder.href, './');
   }
-  return decodeURIComponent(fileLocation.href.replace(baseLocationFolder.href, './'));
+
+  const fileLocationWithEncodedPercents = encodePercentSigns(fileLocation.href);
+  return decodeURIComponent(fileLocationWithEncodedPercents.replace(baseLocationFolder.href, './'));
+}
+
+/**
+ * Encode percent signs (%) not followed by two hex digits as %25
+ *
+ * @param input string to encode
+ * @returns encoded string
+ */
+export function encodePercentSigns(input: string): string {
+  return input.replace(/%(?![0-9A-Fa-f]{2})/g, '%25');
 }
 
 export interface FileListEntry {