What kind of brakes does your bike have?
If discs, swapping out is usually not a problem since the rotor location is standardized.
If linear pull (rim) brakes, there can be a problem with the brake pads aligning with the rim from one wheel to the other. In your case, it may be worth your while to try and get the identical wheels as supplied with your bike.
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"I tell you, We are here on earth to fart around, and don't let anybody tell you any different." - Kurt Vonnegut jr.