You can leave the PIDs as they are really, the only reason to change them would be if some of them were shiny, as shininess uses TID/SID so if you change the original combo, the pokemon will not be shiny anymore and you'll have to find a new shiny PID for the new combo
I just did some tests on my HG save file. Changing TID/SID didn't affect the legality of already caught pokemon, though stuff like shininess changes due to the new combo.
If you edit your TID/SID then the game will just "accommodate" to that and generate regular, legal PIDs for the new combo