Shimano Ultegra CS-6800 11/32 replacement?
I think you must be referring to the new cassette on the second set if wheels.

Sprocket spacing remains the same on Shimano 11 speed across generations. The new Ultegra R8000 cassette will work perfectly well with the 6800 derailleur, maybe even a bit better.

The only trouble you may have is that the cassette may be in a slightly different position on the second set of wheels.