For location integrated with the POS system modifiers cannot be removed from the item. When the sync is run it will add the missing modifier group back to assigned to the item.
Instead of removing the modifier group you can select to Hide the modifier group from the item.
Login to OrderCloud
Select Manage Stores
Select the Location
Select the menu
Select the item to edit
Select the Modifier Group
On the Modifier Group select the Action button and Hide all options for this group.