I would say it IS trivial. Just search for the desktop.ini files in your 100 folders and delete, rename or edit them.
BTW:
Why do you mark your directories with the read-only attribute? This is one of the prerequisites that the desktop.ini will be activated.
I think the software created a parent folder marked read-only that propagated.
Deleting desktop.ini resets columns displayed and column widrhs
There are 2 things: first, I would make the software kick the habbit of creating such puzzling folders.
Second, it would be interesting to see what happens if you delete a desktop.ini after you have renamed a folder. Which name does the folder show then? The old or the new name?
It reverts to the directory (old) name
To achieve the goal to see the real name it is sufficient to disable "Read-Only" of the folder.
Just open a windows console window and type
attrib foldername (incl. path) -R
Or you can edit the desktop.ini and remove the section
[.ShellClassInfo]
I hope this isn't a problem for anybody else. That's quite a clunky workaround