The PowerDeleteSuit fork I used had no problems editing 2y old comments. I did a websearch for my username and chose a custom time for the results, which I set to between one day before I created my account and two weeks later. The oldest comment I found by doing so is from ten days after I created my account, and it is edited like I instructed the script to do. Wasn't a popular comment either, with just 3 upvotes. I think I'm in the clear!
I just tried it for myself, it only made 63 requests to delete 12 comments. These were in my profile, they're ones that have reappeared after being deleted previously.
Meanwhile, if I look in my GDPR files up to where I've got so far with shreddit, the comments are still there, completely untouched.
Maybe you don't have too many comments, so you're within the 1,000 comment limit across your different lists? It's impossible to be sure without having the direct links, either from a GDPR request or the Pushshift backup.
Thanks. That's the same version I used. :( Glad it worked for you... I'll try again tomorrow and see how it goes. My old comments are still hanging out there.