If you're using a script to do so, make sure it's handling API limits specifically for "edit" calls. I realized after I tried overwriting mine that it was quietly skipping a bunch of comments, presumably because there is (allegedly) a 1 edit call per 5 second rate limit. Since adding a 5 second delay between each re-write, it seems to be working for me.

I ran into this issue with u/j0be's Power Delete Suite, I ended up writing my own script to do the job.