I think there's a very good chance he'll be working on Apple Store design, alongside Angela Ahrendts. I think there's a very good chance she'll want a redesign and, for something so critical to Apple's success, Ive will definitely want to be involved.
He was involved in the design of the new Apple Watch display tables[1] that have arrived in Apple stores, as mentioned in the fairly recent interview with Ive in The New Yorker, so I don't see any reason why he wouldn't be involved in store design, too.