My suggestion to you is this, find another 6.8 ammo that IS available, see what your rifle likes. I'd do a very thorough cleaning of the barrel to remove all fouling (carbon, but especially copper) to see how your barrel responds after some fouling shots.
Who's to say that there will be no more good offerings of 6.8 ammo (factory loadings)? Why dispose of a GOOD upper for that reason alone?
Why not build another upper for a caliber which is more available to you and set the 6.8 upper aside until you find ammo once again? Shoot the other upper with what IS available for the time being.
If you KNOW your 6.8 is effective for game, and recoil between 5.56 and 6.8 is similar, why not use a 5.56 upper for day to day range time/practice/training and save your 6.8 for hunting? This way you're not burning through precious ammo which is hard to come by at present.
All you really need for training muscle memory is a .22lr.