TimeQuest Invalid Path / Mis-analysis

Did you have a false path on one of the registers and it was merged with a register that didn't have it? Quartus shouldn't be doing that. Or is it a case where neither register had a false path, and they were merged, but when you went in the path didn't make sense? I would just add a false path from the original reset node, and this should cause synthesis to preserve it and not merge it. (If the second register has a similar false path, it might merge them, which would be fine)