Stereo Micing 2x12 Combo Amp?

I close mic'd up a 2x12 combo chorus amp with 2 mics just to see if one side was any better than the other and when I played them back I realized there was a definite phase difference between the two sides, not exactly 180 either (fluctuates from 90-120 on phase meter). If I play them back panned center the sound partially cancels out, flipping phase 180 doesn't help. But If I play them back panned hard left and right I get a really nice stereo image of the guitar.

Any thoughts on if leaving the track as stereo has any downsides with regard to phase issues later in the mix or should I just keep it simple and pick one of the tracks and make it mono?

I think you need to check the mix in mono and see what happens then decide if the change is worth leaving the tracks as is or trying to time align them or ditching one of the tracks. I usually don't put mics on separate speakers like that because of the problem you just mentioned. If I double mic a cab I put the mics on the same speaker. But I've seen people do it all sorts of ways with success so I guess the answer is "it depends".