I’ve been playing around with something that codinghorror posted to someone else, but maybe this might work.
It’s the read list in the activity tab. It keeps a list of everything you read, It doesn’t disappear. It changes color when you’ve read everything in the thread. It takes one more click but it displays well on my phone. It updates with stuff you read, so it doesn’t disappear stuff.
You could bookmark it or hit your avatar, then profile, then in the activity tab, on the left side, there’s a ‘read’ list.
Could you explain a bit more what the site getting confused looks like or does?