HG PAL English (same as USA) Action Replay code all badges messed up

Hi all,

I had Action Replay codes enabled on Pokémon Heart Gold, the codes were unlimited items (max) and all badges. Somehow those two messed up my game.

I can't get the ledgendaries (after story ones), and when I talk to Oak, or. Blue they say that I have only 4 badges from Kanto, or not all badges. What should I do?

Kind regards,
Procyon