Hi t.spett
There should be no reason to delete any users if the clone file has everyone in it that is needed.
When you apply the clone, it does not add users, it wipes all the users and adds everything in the clone file.
So you would only have to do anything manually once on one device, make the clone of that device's templates, then apply that clone to all the rest of the fleet, there should be no reason to even go on the Scan tab after the first machine.
And I agree about the delete option, there should be at the least a "delete all" option, if not a line of check boxes to select all, or multiple and then select Delete, Export, Import just like the address book does.