Just to confirm we still have this issue with Persistent comments as you noted so keep that separate in the future 
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Unable to remove about 3k comments.
Response to @robin.gierse
“What I have to say: Why would you use persistent comments in the first place?”
We use it in multiple scenarios both with automation and manually. We use persistent both with ACK’s to avoid important info/case number/status getting lost after state changes.
Under normal conditions (before this bug) old persistent comments were sporadically deleted manually after about 100 days trough a dashboard.
If you have any input for an improved work-flow i’m all ears.