Miscellaneous charges are synchronized only between the intercompany sales order and the intercompany purchase order, and synchronization always takes place.
If the field is selected on the intercompany purchase order or the intercompany sales order, you can manually add a misc. charge to the intercompany sales order or the intercompany purchase order. Otherwise, you cannot.
If the field is not selected on the intercompany sales order, you cannot add a misc. charge manually to an intercompany sales order.
If the field is not selected on the intercompany purchase order, you cannot add a misc. charge on the intercompany purchase order.
If the field is enabled on both the intercompany purchase order and the intercompany sales order, you can manually add misc. charges to both orders, potentially resulting in many misc. charges added erroneously.
The best practice in order to avoid these types of conflicts is to allow misc. charges to be added either to the intercompany sales order or to the intercompany purchase order, but not both.