Nautilus doesn't merge folders with the same name if one of them has uppercase letters and the other doesn't; if one is called "Folder" and the other is called "folder" then Nautilus wouldn't merge them. I have a large amount of files that I need to merge, is there a script that would allow Nautilus to mass merge them all? If not, is there another way than manually renaming all the folders?
It is by design. File and folder names are case-sensitive in *nix systems.
To complete the answer, here is a script that does the renaming for you.
rename 'y/A-Z/a-z/' *
This should rename all files/folders to lowercase.
NO, you can't simply merge them.
In any Linux or Unix (including Ubuntu), filenames and folder names are case sensitive. So two similar directories but with different case can co-exist.
You need to create a shell script to rename them ..
( I will see if I can find the time to write one. )