You have to be careful with a Nissan dealer working on the car. They will note a fault, pull out the book and look up the steps required to rectify it. They are required to follow this procedure because that's what keeps them selling cars for Nissan.
If the loom is still damaged, they might still be getting eroneous signals from the TCM and the book says "replace the TCM" and the only way for the dealer to do that is to replace the gearbox. Actually they can just replace the valve body ($2,000) which contains an unprogrammed TCM - I have done this so I know what I'm talking about - but if the gearbox IS stuffed, you would be better off getting one from a wreck. That's what I did after replacing the valve body in mine didn't work.
However, I would question the need to even touch the gearbox. If there was loom damage, maybe not all of the damage was found?
Is the gearbox selecting gears acceptably when driven smoothly?