For us, the linkage between the requesting site's PO and the shipping site's SO is often confusing.  I often have to instruct users to close the originating PO, not the SO.

Hello, 

This is a reported issue and there is a workaround. There is supposed to be a fix for this in a future release.

This happens when an inter-company sales delivery is created for full quantities, then the inter-company Preceipt is created for partial quantities and thereafter a Customer return is created and linked to the Sales delivery. 
This results in the end user being unable to close the inter-company PO. 

Waiting for a fix in a future release.

Workaround:

1. Create purchase receipt for full quantities. Selecting the Delivery from the left list
2. Create a purchase return for the missing quantity. Selecting the preceipt from the left list
3. Create the Customer return selecting this purchase return from the left list "Supplier return selection"

Note: this workaround is for future transactions.

8006108569 

ID:83950Last Modified Date:3-7-2018  

So the PO does not have a receipt. If we made a Purchase receipt would that allow us to close?

Yes, that method should work as a workaround until a full patch is released.

Also, If I created a receipt would that not make a an accounting obligation where the system would be expecting to pay for this?

Even if I create a receipt for the PO. I still get the error below. Its looping back to the sales order. 

SO011730017 : Processing not possible:  Closing not authorized

I would suggest you contacting support so they can take a deeper look into your system configuration.