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I’m not sure if it’s a coincidence, but I raised a case with the ICO in the UK, and today they got back to me asking for all my communication with Reddit. Also today - after a month of silence - Reddit also emailed me with this
If you’re in the UK and had been affected by posts being restored, I’d recommend contacting the ICO. It takes less than 5 minutes
Regarding PowerDeleteSuite it's because it hasn't been updated in multiple years and since then (like a year after the last PDS update) Reddit added a cooldown for editing comments. I assume the same exists for deleting.
So when you run the script, occasionally you hit the 5-sec cooldown but the script just keeps moving, thinking everything is okay.
I just used the tool last week and it deleted 3500 comments successfully. A couple of times it encountered errors, but it stopped and asked what I wanted to do before proceeding.