NOOBest question evar... do I need all SD files inserted forever?

I searched it and searched it, and I know it's NOOB, but I can't find it so have to ask... Once I did my Indiana Pawns unlock, I had trouble, and now I have MAJOR trouble... regular games still boot fine, but NO homebrew loads... I already cleared my SD. Do I need to redo the hack and keep all the files on there or what? Everything I try to boot (Helium Boy, etc.) all freeze.

What am I doing wrong? Feel free to be as comical in your slams as you're able, but I really am just trying to figure it out, so don't slam me too hard. ;)

You can safely delete all the files, the only things you will need are some apps
and for your problem with homebrew not loading, it may be because you don't have the correct sd card setup, go here and do some reading on how to configure the apps