Praetorfable

Hello, I just merged my red and blue server accounts from about 2 years ago, and when I logged in I found myself unable to move Pokemon from my Party to my PC and vice versa. Before I had stopped playing I had just made it to Johto, and so I think that the Kanto Pokemon from my other account was merged and now can't be moved. Anyone able to assist with this problem? Thanks, PraetorFable