This was originally going to be a "please help me" post, but I found a solution on the dot com boards so I just wanted to share it all with you.
I had an order of around 50 items that I wanted to send a combined shipping invoice for. Ebay only lets me add 40 items to the invoice. Ok, that's fine, I'll add the rest to the second invoice. NOT. Every time I tried to select the remaining items to add to a second invoice, it would keep loading the original 40 into the "invoice editor" screen (the ones I'd already sent an invoice for).
Frustrated, I did some searching and found that the way to beat this is to create your 40-item invoice, then mark as payment received. That'll take it out of your "awaiting payment" screen, and allow you to send an invoice for the remaining items. Then once the second invoice has been sent, you can re-mark the original invoice as payment not received. And bam, problem solved. Buyer has two combined invoices to pay, and you are headache-free (not really).
Make sure to communicate with your buyer beforehand, so that they understand what is happening and know to wait for your second invoice before paying for everything.
Hope this helps someone.
