In-frame, what to do with ECM? Need guidance

[Waterloo]

My motor is coming along, hopefully be up and running by Friday this week. But, here is the question the owner of the dealership has asked me, and I don't know the answer.

When they near the end of the in-frame, they normally do their thing on the ECM with a clean program and whatever else they do. I have the @m*m^2 on there, and do not know how to proceed? I was going to ask Unilever to do a fine tune on her, but what do I tell, or allow the dealer to do? They know about the MM. Need some guidance here.