I did that, and it had the same result as the first time.
I found what I was looking for
here.:
SD:\Nintendo 3DS\*random letters and numbers*\*random letters and numbers again*\extdata\00000000\000002cd (this is your themes data folder)
SD:\Nintendo 3DS\*random letters and numbers*\*random letters and numbers again*\extdata\00000000\0000008f (this is your home menu extdata,it contains home-menu savedata and cached icons for applications)
These are only for US versions, apparently.
I deleted these folders (only after backing them up), re-inserted, and all it had to do was set up the HOME Menu management info again. Well that and I had to unwrap an ungodly amount of things.