Anything done to change the muzzles of a double gun has the potential to change POI, thus affecting regulation. However, when both barrels are shortened their relationship to each other is not changed. That relationship, and proper choke work, is what allows regulation. Regulation does not mean the gun will shoot to POA, it just means that both barrels shoot to the same POI. POI of both barrels, together, can be adjusted to where needed.
If the barrels are shortened a reasonable amount due to muzzle damage, and most of the choke remains, and the muzzles are faced properly, I would not expect a change to regulation. But, I've messed with double guns long enough to know to not make guarantees concerning regulation after drastic surgery.
SRH