Well, crap. Here's the response from the developer:
link to vbulletin.org thread
So the notifications still work and show up for people, and the mod is still working fine for any new posts. But some older posts will not have the mentions visible anymore. What's a little strange is that it didn't wipe all of the older ones; I have a hunch that's because the "rebuild post cache" feature probably checks to see if it really needs to rebuild that post or if it hasn't been viewed/changed since the last time it was built, and maybe those are spared. As from the developers explanation of how it works, it seems like it should have wiped out every mention in any of the rebuilt past posts.