I don’t think they did. Unless you have evidence otherwise, I think this is a rumour which comes from a misunderstanding of how deletion tools worked. Until recently, the api only provided access to 1000 posts per feed, i.e. 1000 most recent comments in your /comments/new feed. So if you try to mass delete “everything”, you really only delete the 1k posts from each feed, which can leave a lot of your posts/comments unfindable. This has been a commonly-complainaed about limitation of the API for 15 years. But people would run a “mass deletion” tool, think they’d deleted everything, then later find a comment that wasn’t deleted and they’d get all conspiratorial. I seriously doubt reddit cares about your comment that much, much as we love to hate them.

I personally wrote a script to scrape search engine results for a “myusername site:reddit.com” search, looking for my comments to delete. After running various mass deletion tools which claimed to have deleted everything (and made my profile look empty, since all feeds had been exhausted), I was able to delete tens of thousands more comments which weren’t findable via the API. I… used reddit a lot.

The API has recently been updated to allow more (?) posts to be visible. Since that change I was able to view a couple thousand more comments via my profile, so deleted those too. If you have that volume of posts it’s really just a case of trying to find them all however you can. The api has always been limited.