Programming brand new ECM and TCM

I've been trying to surface information on the procedure for replacing an E98 ECM (and a T43 TCM). The physical swap doesn't seem to be tricky, but for a customer with a tune and an AutoCal, can they simply bolt on the replacement parts and then do a full flash of their stock or tuned config to get back up and running?

Dealers charge an absurd price for what is actually pretty affordable hardware. I'm curious if it requires an initial flash from the dealer before an AutoCal can interface with it, or if the AutoCal can actually set all the necessary parameters based off a tune file.