Yes. Handling the carburetors WILL make the sync get out. You must set sync after each carb removal and before tuning for all speeds.Perhaps something that might be fixed with a good carb sync?
All it takes is a touch of the adjusters and it's out of synch again.
The instructions for jet kits only give you a starting point for the fuel mixture screws. Called the "bench setting". The same is true for jet needle clip positions and even main jets. Although the instructions are usually pretty close for main jets.
It is not at all uncommon for fuel mixture screws to end up being as different as up to 3/4 of a turn different from one to the other. Sync FIRST, or you'll never get them right.
If you do not have an Exhaust Gas Analyzer the only way to get the fuel screws set correctly is by running the bike mostly on the idle / slow speed circuit then 'read' the spark plugs. Even with an EGA reading spark plugs will be more accurate.
For all other speeds an on-board EGA is useful but again, reading spark plugs is the way to get it Spot On... AND, You need to use new, unused spark plugs pretty much after most every adjustment made.