It should stay unlocked even if the local save is lost. Are you sure you used the same Kongregate account when you played Incognito and after? Please check my PM.
So... summing up... This game is all about FARM FARM FARM FARM FARM FARM, and DULL bosses (at least up to level 30, all the fights are THE SAME) ... Quite boring... really... There's NOTHING to do besides farming. If you like farming - this is your game :) If you like playing... leave it.
It should stay unlocked even if the local save is lost. Are you sure you used the same Kongregate account when you played Incognito and after? Please check my PM.