This is a common problem. Sometimes MQB remote key (i.e from a Golf VII) starts engine but remote not working after program key with obd programmers.
Here are the possible solutions.
Reprogram the key and remote works again. If you replaced microcontroler, key has to be re learn , means you need to reprogram key to immo . I will be good to add extra key .
program them with VVDI2 but Autel IM508 also will do the job
Note that after programming is possible both remotes stop work if this happens reprogram again but program first this that was second.
There is a manual resynch with an already programmed MQB key.
It just loose synchro like many VAG remote when key battery come bad and need change.
Update MQB remote Sync (after repair PCB):
1. Lock the car
2. Press Unlock 2s the key need to sync
3. Insert the key in the driver door lock, turn to Unlock (Left) then Lock (Right) then Unlock again.
4. Press Unlock button on the remote key (key still in the door lock)
Car signal light flash to confirm.
Some people did and work perfect. No need reprogram the key.
Do not mess with the mqb key , as long you have a start, suggest to you to add new key, otherwise you will have to treat it as all keys lost.