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Or you can shim them in to the correct position, assuming they are six bolt. And you don't need negative shims :)
I had this problem with XC race wheels on what is now Branwen's Cannondale - it was actually a real pita because the hope and old cannondale hubs put the rotors in such a different place that you couldn't even get the wheel in if you tried a direct swap. Ended up shimming the shit out of the cannondale hubs.
The calipers were direct mount IS, so no, no adjusting in five seconds there.
Use the same brand of rotors on both sets. If the hubs put the rotor at different offsets, that's 2 secs with a 5mm allen key, assuming it's a postmount caliper.