That is a normal business transaction and you can do the following.
Business central allows using Item charges on any Purchase Invoice or Order and you can still apply that charge items to the Purchase Receipt line from another PO. To explain let's take following example.
You raise Purchase order 1 with Vendor A and you received items from Vendor A let's say Purchase Receipt number was 1001, now you booked invoice and closed the Purchase Order.
Now Vendor B who provided transport/shipping etc. has raised you Invoice.
So what you can do is in while recording Purchase Invoice of Vendor B you can use Item Charge to record the expense.
Go to Item Charge Assignment and find the option of Get Purchase Receipt line, there you will find all the receipts that is posted, find the 1001 and fetch all the Item lines(if multiple otherwise single line), do the assignment and post the invoice.
Impact - The Purchase Invoice for Vendor B will be posted correctly and the charges will be added to the cost of item purchase in order 1, receipt 1001 from vendor A.
This is standard practice in business.
Regards,
Dhiren.