Folks, it's not that Reddit is undeleting comments or anything. I fought this all day today (see https://kbin.social/m/RedditMigration/t/45417/Anyone-have-experience-with-deleting-comments-to-see-older-comments#entry-comment-190482 ) and I figured out exactly what is happening.
Reddit is so dumb! They have an 1000 limit (on posts, comments, saved, etc). See for example https://news.ycombinator.com/item?id=17647915 and https://stackoverflow.com/questions/42940262/getting-more-than-1000-search-results-upper-bound-with-praw and even in PRAW's own docs, for example in https://praw.readthedocs.io/en/v3.6.2/pages/getting_started.html
Any single reddit listing will display at most 1000 items.
So what happened is that redact.dev can only delete the most recent 1000 comments of OP. But those subreddits have comments from OP beyond the limit, which no longer display in OP's own profile/comment views.
https://shreddit.com/ reports the same thing but they are more open about it.
They explicitly say that you need to give them an archive upload (from reddit's data retrival request) in order for shreddit.com to delete everything.