Thanks for the replies, I've figured it out though. The "Thread Removed" message in the moderator logs was caused by moderators merging threads. Apparently, it makes two entries...one stating "Thread merged from multiple threads" for the thread title to which both threads were merged to, and the other stating "Thread Removed" for the thread title which doesn't get used.
So, it was false alarm. Nothing was actually getting permanently deleted except for what would be an empty thread after the merge. It was just a matter of how vB enters the mod actions into the log. I'm not sure how I didn't notice that at first since there was always an adjacent entry by the same mod stating "merged."
But, thanks again