Your toilet probably won't seat properly. The toilet sits on the floor, there is a circular depression in the toilet that gets filled with the wax ring which presses down on the flange to seal things. If the flange sits too high, the toilet will rock or there will be no room for any wax and it will likely leak. Three choices if it doesn't sit flat...tear out the flange and lower it (best alternative), look for a toilet with a higher opening (not likley but there are slight differences), or raise the toilet back up on a platform. If it is a cast iron flange and pipe, lowering it isn't too bad nor is it if it is pvc, especially if you have access from below. If you do, and it it cast iron or pvc (or abs), you could cut out a section and rebuild it to the proper height.