Yeah, that's one thing Altium designer could do better at.
Sometimes when changing multiple things at once AD will get confused when you do the next PCB update (with regard to what matches to what on the pcb). Then you get the unmatched designators message and have to deal with it.
It happens because AD doesn't try to match things up until you do the next PCB update. So if you have changed or moved net/trace A -> B and also B -> A then it isn't sure which way to jump and has to ask you.
I try to limit the number of serious layout changes between each PCB update which mostly gets rid of the issue.
It would be nice though, if the designators remapping window gave more info so you could figure out what was supposed to match what.
(Unless there's some super easy way to fix this issue that im not aware of.
Altium is full of useful features people don't realise exist until years later
)