Your explanation about the files is what I believe as well, however you would have thought they would put some safety mechanism in place to stop people semi-bricking there PSP, also the error you get while overwriting is a failed CRC check, not a write protect error.
As to your issues, hide corrupt icons isn't perfect, you may need to re-kxploit them, hard reset isn't perfect as well, those error's should be handled by the homebrew developer.