The combined shipping function has always been a bit problematic. Generally your orders page will reflect items eligible for combined shipping. What does your current orders page reflect? If your buyer has paid what do the order details reflect with regards to what the buyer paid for shipping?
I am not sure of the exact details of the 5 items you have to pack and ship but probably best to contact the buyer and work with them on the details of the combined shipping. If they received an invoice from eBay and it reflects individual shipping for each of the 5 items let the buyer know what you are able to "safely" combine, and approximately how much of the shipping cost you will be able to refund. Have them pay the invoices, pack and ship the items and issue a partial shipping refund.
I have had to work through a similar situation a couple of times but not so much from a safety reason but from package size an weight issues.
