3DS Homebrew & Other Modifications Gone

Stargazer58

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Recently I took out my SD Card to use a save editor for a game. When I inserted the SD Card back (after properly ejecting SD Card), the home menu theme was the default theme and all homebrew was gone. I'm not sure what happened, is there anything I can do? I didn't any files pertaining to homebrew (only modified checkpoint folder in the 3ds folder).

EDIT:
When opening system settings the sys prefix before the version number is still there and when attempting to acess the data mangement screen for Nintendo 3DS apps, a popup says "The SD Card software-managment data is corrupted. Reset it now? This will delete all software and save data." Should I backup and reset the data?
 

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