There is no facility on eBay to combine sales from two different IDs on one invoice, so the only way you would be able to handle it is reducing the postage on each individual invoice, you will have to be wary of that, though, as if you send an invoice for one lot of items with 0 P&H (so that the other invoice is the only one with postage costs), it would be possible for the buyer to only pay for the 'free post' items.
The one alternative is to invoice directly from PayPal - you will have to generate a manual invoice, put in all the necessary details (eg eBay item numbers and a description), then a single, combined postage cost. Some buyers are a little wary of not using the ebay checkout, but if they are regulars you may be able to explain to their satisfaction that it's on the level (i.e. still well within eBay policies, and doesn't compromise their protection).
