diff --git a/querysync/java/com/google/idea/blaze/qsync/AffectedPackagesCalculator.java b/querysync/java/com/google/idea/blaze/qsync/AffectedPackagesCalculator.java
index 9b69bcf660a..fceea387769 100644
--- a/querysync/java/com/google/idea/blaze/qsync/AffectedPackagesCalculator.java
+++ b/querysync/java/com/google/idea/blaze/qsync/AffectedPackagesCalculator.java
@@ -95,6 +95,11 @@ public AffectedPackages getAffectedPackages() {
       context().output(PrintOutput.log("Edited %d BUILD files", buildFileChanges.size()));
       for (WorkspaceFileChange c : buildFileChanges) {
         Path buildPackage = c.workspaceRelativePath.getParent();
+
+        if (buildPackage == null) {
+          buildPackage = Path.of("");
+        }
+
         if (c.operation != Operation.ADD) {
           // modifying/deleting an existing package
           if (!lastQuery().getPackages().contains(buildPackage)) {