TimeQuest Invalid Path / Mis-analysis

It's not a mistake by TimeQuest, as it's just looking at the physical layout.

The one place I see stuff like this is with merged registers, i.e. two might have the same behavior and Quartus merges them, but only keeps one name. It also merges shift registers when making altshift_taps blocks. That all being said, it's only synchronous signals I've seen this confusion occur. A recovery violation involves the asynchronous reset, which has to be common between the two nodes. Actually, thinking about it more, maybe there are two identical circuits that make identical resets, and those got merged?

Maybe try Assignmetns -> Settings -> Anaalysis & Synthesis -> Remove Duplicate Registers = Off. I'm not saying that should remain off, but if the problem goes away you'll understand why.