Theoretically, worst case scenario is that you had periods of rich A/F's during your shifting, and if the tuner compensated for this (doubtful, but possible), then you could now have periods of lean A/F during shifting. It also depends on your EMS method. Cobb AP? Chipped? Piggybacks tend allow the stock ECU settings free reign for compensation on fluctuations in A/F, so if this is your case, you'll be fine. If not, again, contact your tuner to be sure, and be sure to ask him questions along these lines.
I wouldn't worry too much though.