The lack of indexing and privacy status of the subs likely contributes - but it's also API rate limiting for many of the automated tools like Power Delete Suite.
It will appear that your comments are gone, but the limiter prevents activity from being permanently written over X calls per minute.
I think people may need to wait. Here's what I've read and seen myself so far:
You can only edit/delete so many comments as it seems reddit only indexes the last 1000. After editing/deleting everything you can, you can see you still have unedited/undeleted comments by searching your username like:
site:reddit.com "usernameHere". I saw plenty of comments going back years (I have a 14yr old account) that I wasn't able to touch.The strategy seems to be to be requesting your data from reddit and then use the comment ids contained in that export to target them for edits/deletes via the API, assuming it's still usable for small scripts like the ones we want to use.
We're tracking our requested/received dates in this thread if you're interested in adding yours to the list.
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