Why did Canon DPP ignore and then lose dust removal edits?

I had two RAW files, in the same folder, taken with the same Canon camera. Then spent ninety minutes in Canon Digital Photo Professional (latest version) using the dust removal tools ("light" dust removal, and also source clone). Then used batch process to generate JPEG files from the finished edits.

The first JPEG was fine, showing none of the dust spots that I’d removed. The second JPEG was a mess, showing every spot of dust that I’d spent so much time carefully removing. I tried regenerating the JPEG for the second image, but no change. Tried going back into dust removal mode (which was still showing all of the dust as removed), making a trivial edit, and saving again, but still no effect on the resulting JPEG. Then I exited DPP and reopened it, to find that now even in dust removal mode none of my retouching had been kept. So that was forty-five minutes out the window.

So my question is: did I do something obviously stupid to lose the dust removal changes (even though I saved the RAW file changes several times while the retouches were still visible), or is this a known bug in Canon’s RAW processing software?