New Hunt wheels

Hunt wheels are suitable for centrelock rotors which I prefer to 6 bolt, I don't see how a centre lock rotor could not be compatible. Perhaps you could post a picture.

If you wish to use 6 bolt rotors you can buy a centrelock to 6 bolt carrier, which I have doe to use my hope rotors.

As Kil0ran said it sounds like you are have a 9 or 10 speed cassette. The standard Shimano freehub fitted to Hunt wheels is intended for 11 speed but usually comes with a spacer for 10 and 9 speed cassettes. The spacer looks like a very small metal ring the same diameter as the freehub body and usually comes with the wheels. You simply thread the spacer ring onto the freehub body before the cassette and finally the cassette lock ring.

All Hunt wheels are (at least) 11sp, how many cogs on your Synapse. Some 10sp cassettes will need a spacer to shift the cassette to the right position. 

Centrelock is centrelock so should fit, can you send some pictures? When you say it's not fitting, what's the issue? Not lining up with the brake caliper?

It sounds like the wrong wheel to me or possibly the wrong cassette (e.g. 10 Vs 11 speed). I wouldn't expect to have to totally redo the gears for a new wheel, usually just a minor adjustment to get it spot on. Also, centrelock and 6 bolts are different standards which means either getting the correct rotor/wheel or possibly using an adaptor.

Seems a bit odd.  Are you sure you have the right thru axle or qr?

It's not unusual to have to adjust the derailleur when you swap wheels. There's sometimes minor differences. But not usually so much that you can't get the lower gears... best do a setup from scratch: set upper and lower limit stops, then adjust cable so it shifts properly. Shimano's an Campag's tech docs explain how to do it, its reasonably straightforward.