> for some reason, whole conversations get reset to a single timestamp.
What do you mean?
There is some action that moderators can take that throws one of yesterday's articles back on the front page and when that happens all the comments have the same timestamp.
Submissions put in the second-chance pool briefly appear (sometimes "again") on the frontpage, and the conversation timestamps are reset so it appears like they were written after the second-chance submission, not before.