No issues. Whenever you disconnect the battery (I think for at least 1 min), the ECU has to relearn anyways. Thus why you can't simply pass emissions testing by quickly disconnecting the battery to clear a CEL and then get the test done once reconnected. The car has to run thru a full prep cycle (readiness test) to ensure all parameters are met and cycled thru. Go ahead a disco it for the winter but obviously leave it on a charge...
BTW, I hate hearing all this winter prep crap. I'll have to put my car away but HOPEFULLY [fingers crossed] it won't be until Dec????