There is a campaign doing the rounds about revised coil packs. May not apply to your car, though.
The reason they swapped the coils was to see if they could 'move' the problem elsewhere. If the missfire re-occurs, and it is on cyclinders 2 and 3, then that's where they'll look. If the faults are logged on 5 and 6, which are the suspected faulty coil packs, then the dealer will most likely replace those, and theoretically rectify the problem. It's just a process of elimination, with you doing the testing.
'07 Transporter 1.9 TDI
'01 Beetle 2.0
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