I noticed this earlier and basically, it messes up your account in multiplayer games because Kongregate doesn't keep the original name as a login name for purpose of games, they just pretend it never existed and the API sends the new ID instead
-_-

To fix this in a generalized or automatic way seems nearly impossible without opening the door to some type of exploit, so I think it needs to be done manually. It may be possible to do this sooner than I originally said, but still not sure exactly how stable the current idea is, which basically amounts to linking the new account to your old collection/mastery/etc and manually copying over most of the other relevant stats. I'll have to do some testing to make sure that's a safe thing to try, but it would mean this can be resolved way sooner. There may be some collateral damage in the form of small details since I probably won't copy everything, but hopefully all of the most important things can be fixed.