They don't have to, but they MIGHT, as a courtesy to you, the customer, since the car is in the shop anyway, if updated calibrations are available. Nowadays, many parts failures are addressed with updated computer logic to decrease chances of part failure in the future.
So plan on checking the strategy code if you are tuned, after you get the SHO back. If it has changed, get an updated tune from your tuner. Load the updated tune to the SHO so it will run correctly. If a 3 bar MAP is involved, reinstall that just prior to loading the tune (i.e., no driving w/o tune).
My advice would be, if you want to play it safe, is stay stock until you complete your trip and are back home. Least amt of headache that way.
If they do not update the strategy code/PCM calibration, that would be the best scenario! Pick up your SHO and go
