Yes I though the same, I though maybe some files had to big names (Harry Potter and ... + 12 languages), I tried to remove those files but no luck neither
It seems kind of like the layout of folders is done like the binary bullet points in Microsoft Word where sometimes names will either get centred for games or stay on the far left corner or go to the far right by themselves. Back on the really old EDGB I had to put 1, 2, 3, etc before each GB/GBC/ folder as adding 1. 2. 3. caused the . to be a square thankfully the X7 corrected this.
I remember once when I had my old Super Card SD before its battery ran out I had to label each folder with a 1. or another number as each time you renamed a folder it would appear at the end instead of the front... this was useful when the Disk IO error happened as it saved me having to extract every rom folder all over again, this notepad document sums it up well...
https://www.sendspace.com/file/8gdvelFor the GBA Everdrive this can also be done if I remember years ago you just would need to add some extra text at the end of the folder name I think its either a number or you delete a word from it normally it will always move that folder to the end of the list, likely you wont need to do this unless you ended up removing a Disk I0 error folder and don't want to delete the entire card just to put the folders for each format back in order again.
So in short if you had 4 folders that were say
4 SNK Neo Geo Pocket Color
4 Super Famicom & Super Nintendo/
4 Translations
5 Tools & Service Test Carts/
and the SNES one corrupted and it then just had SNK, Translations, and Tools you wouldn't need to delete the other 3 folders to get SNES back up there just change the end name of the folder and each remade file will always appear at the end of the list then just do it with the rest until SNES is back in its place when you don't rename it.