While I agree that a full re-install is likely the safe bet, FileOrder.ini is a records file for the GUI and mostly inconsequential. Neither leaving it nor deleting it will have a positive or negative effect on the game.
Viewing post in Aric's Expansion Rebred
You are welcome to look at modpanel.gd and try to find that mechanic; however, you are reading between the lines to find mechanics that don't exist.
"func show():" refreshes the mod list GUI, and uses loadorder to sort the mod line, determine which mods have pressed buttons, and get the order number shown beside the mod.
"func _on_applymods_pressed():" uses loadorder without any checks for "enabled" or "disabled". The first thing it tries to do is erase all currently installed mods, so it doesn't care what is installed. Next, it iterates on loadorder to install mods one at a time.
Thus, removing the mod from the load order has a total functional result of forcing you to add it back to the load order.