as long as you are on 3.2 or lower, the savefiles should remain intact, back them up just in case.
just MAKE SURE you only delete the pirated channels, not uninstall, using any of the available "uninstallers" also deletes saves, I believe. Of course, if you back them up to SD like I already said, you dont have to worry, and can go ahead and do a full uninstall

so yes, backing them up to sd and uninstalling then downloading and reinstalling works fine.

 

deleting pirated channels through management menu causes no problems Im aware of, except they arent fully uninstalled, which some consider a problem.

if you copy them to SD, and they won't copy back after you buy the games, it is only because you have 3.3, and I don't even think its gonna be a problem. It shouldnt be. You just downgrade if you need to.

 

or just go into GeckoOS, reboot witht he rebooter in there, it should let you copy the saves that you couldnt usually copy before, copy your savegame for that save game, uninstall the wad, buy game, put savegame back.