Ah, got it.

The "Mark as Read" feature was rudimentary and didn't work very well. We could look at storing whether a user has read a post, and use that to provide an indicator if there's something new. I can take a look at it.

In the meantime, I'm planning to show all replies under the threads again. I need to limit it at some level, but if you can see all replies on the forum index for 99% of the threads again (and the visited links) maybe that solves it.