It looks like people's comments are coming back because they didn't get deleted. From discussion in other threads and on HN, it looks like the comment deletion scripts can't delete comments from subreddits while they are privated.
If you tried deleting comments during the blackout and then some of those unprivated, you would expect to see those comments again.
There is a lot to be upset with Reddit about, but this doesn't seem to be one of them. (at least based on what I've seen)