just had a look at some numbers from 2011
if Labour had taken Ynys Mon, but the regional votes remaining roughly the same*, Plaid would've got an extra list seat, with the Lib Dems losing their only seat in North Wales. Labour would have an overhang of one since they got no list seats.
I'm assuming that they don't go and recalculate the list seats if a byelection changes things in this way?
*Plaid need to stay about 7,000 votes ahead of LD region-wide to keep the final list seat in that fairly improbable situation
Alas, no. By-elections are a wholly alien feature to MMP and are not factored into the seat allocation rules at all. They're just there because of tradition. (See also, by-elections in Ireland.)