If you use JSGME, no need to make back up, JSGME is doing this. Just removed the mod when you want to come back at JSH alone with this tool.
No units are removed, but their names are removed from the filesid.ini
As far as I understand, this file is mainly needed for MP, so I think that for SP, there is no problem.
You can of course back up this file (in data/settings).
You can look at the file "modif files id.txt" to know which units I have removed from the filesid.ini