What I'm asking is would it be possible with my current psp (phat with 5.50 gen d-3 on it) to remove everything from the memory card and begin fresh again without any issues? I want to start from scratch to ensure the errors I'm having aren't related to some sort of glitchy software.

If I delete all the stuff off my card what do I need to do to have 5.50 gen d-3 running on it like normal?