There are several concerns but all are manageable.
1 cassette placement...are both cassettes equidistant? if both line up exactly with the rear derailleur you are fine but if one doesn't and you have to adjust the rear der then you have to shim one of the cassettes in order to equal the alignment...easy task
2 rotor alignment...are both wheel sets rotors equally aligned with the caliper if so fine if not some work may have to be done or if the misalignment is minor it is of no concern...long as they are not rubbing
3 chain wrap, when using the 28 cassette the chain will be a bit longer than necessary but not a big deal, just stay away from gears that magnify the loose chain