I don't know when exactly this happens because I just noticed this recently. After working for a while over a series of days, saving the JSON from the ACRT for a particular web page I'm finding that the original list of 61 checkpoints becomes truncated.
So then I notice something I may have missed or decide something should have been reported on a different ID, whatever the reason when I go back in instead of 64 IDs I may find as few as 40! The other issues are gone entirely. I then have to go back and rebuild the Report from the start, copying data from the previous report to a new report before I can add or move the items I wanted to add or move.