There doesn't seem to be a way to disencumber direct charges on an activated PO other than removing the charge, which works OK if everything on the PO has been shipped and you need to disencumber all the charges at one time. But if only some of your order comes in and you need to pay just some of the charges, you've got a problem. Let's say the total direct charges on your PO is $100 but you need to pay just $40 of that. If you create an invoice and add a $40 direct charge, it pays the $40 but does not disencumber that same amount on the PO. There doesn't seem to be any relationship between the charge on the PO and the charge on the invoice. We're on 2.9.4 but I think this is an issue on all versions.
Marking this Won't Fix as this is now possible in the Angular PO interface as of 3.10.