Anyone know if it will affect performance, or have any downsides to using a second set of wheels (with different discs/casette) on my bike.

I do this – same disks and cassette though. It's easiest if the hubs are identical too as then you don't have to play around centreing your calipers.

You should swap the chain as well (I think?). I run 2 sets and have no problems, though I needed to use some disc rotor shims to make sure the rotors on each wheel lined up OK (though you may get lucky with this!)

These things, from Syntace

As druidh says, I'd recommend sticking to the same hubs to avoid disc position faff. Best to have a chain for both too so the chain and cassette can wear together and in case you plan to run two different cassette ranges.

I'd be more inclined to do it on bikes where it's easy to centre the calipers than with ones where shims need to be used.

even with the same hubs you can still get issues (design tolerances and all that…) If you have problems with disc drag when you swap your wheels, the Syntace shims are an easy way to sort it 🙂

Agree, shims are much much easier than adjusting a calliper each time.

I used to do it, never had a problem not swapping cassettes etc over.

I change wheels purely as a quick and easy way of changing tyres for races etc. If you had to centre discs or change chains then there is no point. It would be quicker to change the tyre!
I've never had any problems but do use the same make hubs/wheels.
If you find your using one set more often, just swap the cassettes over every so often to share the wear. Simples!

If you had to centre discs or change chains then there is no point.

Depends on the brakes. My Inbred has Deore's and all that needs done on that is to loosen the mount bolts, pull the brakes on then tighten the bolts up again. On my Cotic with Hope Mini's it's much more of a problem though as you need to shim the brakes.

but if you fitted the shims in the first place, you'd never have to worry about it again, so you wouldn't need to undo those mount bolts each time you swapped wheels 😉 Trust me, the shims are the way to go (if you need to because of your hubs).

Cheers guys, think that answers what I was after

i shim out with washers to get disc brakes to align with different hubs. i dont bother changing chain or cassette, i have significant chain wear and chain ring wear and jokey wear, but my cassettes are still in fairly good nick, running the lot into the ground now though.