Looking at the thread you linked to I don't think there will be an issue with swapping the barrel, the only issue will be with programming the keys.
Do you have a working master key for both cars? When you say the chip is destroyed, does the key not work any more? If so you should be able to use the old key to program the new one and then it should all work fine.
Actually ACLex makes a good point, you won't even need to program the key if you can just swap the electronics over (assuming it's not broken)