I mean if EU happens all Nintendo stores will be over there, so...
Easiest thing they could do would be do exactly what they've done in Japan and just take out the AP lounge, move that elsewhere. Bob Marley's, hell maybe the movie theatre gets shutdown or some of the space is moved for retail, idk. I think they have options.
Also, this new store they're opening is gonna be very large and could easily include its own Nintendo floor, or half of a floor.