I would think you would want to do the retune with your ECU adapted (as it was when you brought it in) so that the ECU is already adapted for the way you drive and for where you are, ie high or low elevation etc. , then do the tune. It may not show greater numbers but I think true numbers. I mean if the ECU adapts and compensates for things, then resetting it is kinda cheating for numbers in my book. But Im in no way an expert so this is just my 2 cents.
To me adaptation is baseline prior to mods of course. After mods its still part of the gained hp/tq numbers.
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2010 LS3 C6 Silver coupe corvette
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