You might have just let it run past the rate limit.

After it limits you, the script looks like it’s still running, but if you hit refresh, you’ll time out, and nothing past when you’re actually limited, got deleted. It’ll be several minutes before you can start running it again.

I’ve done this for many hundreds of comments.

Every once in awhile, I’ve had a few batches of comments reappear that I can’t associate with a rate limiting error, but I have yet to find comments that come back a third time.

I guess YMMV, but that’s what my experience has been.