A couple things.
The original github for PDS, j0be github, has a bug (or more likely an issue that appeared after PDS stopped getting maintained). So it clicks the button too fast, and reddit doesn't allow that, so the result is that some posts miss the edit/delete.
There are other githubs for PDS out there that have this fixed, adding a 5.1s delay between simulated clicks.
Also, PDS is affected by reddit's 1000 indexing limit, so even if you used a fixed version of PDS, it's possible that PDS won't get everything, even if your profile looks like everything been overwritten or deleted, some stuff might have been missed.
Finally, the good news - PDS simulates clicked on the website rather than using the API and should work as long as old dot reddit is up.