You will just have to navigate the upside down HBC. I've done it before.
Also, you should never install Darkcorp. It's a really bad idea since it replaces every IOS with the same file and might cause compatibility issues, even with games you own. It's not even needed, if you just want to launch burned discs from System Menu you can do so by installing Priiloader and forcing system menu and game IOS to 249. That will still have the same compatibility issues, but at least it's not making big changes to the system.
I recommend using a USB loader instead though. It won't have those compatibility issues, and you can still load burned discs through it if you really want (but why would you want to when HDDs are so much more convenient)
I would recommend undoing everything you did. You can reinstall the original IOS files with Multi-Mod Manager, and use SysCheck (
https://gbatemp.net/threads/syscheck-hacksden-edition.356133/ ) to verify that you got rid of all the patched IOSes.