You say "which were bundled together by eBay", so they were combined? Even though the postage was overcharged.
Anyway, with Simple Delivery the items have to be bought in one transaction at checkout to receive a single postage label for the items to be combined.
SD doesn't work very well for combined items. An alternative is to cancel/refund the transactions and relist in one listing with one postage for the buyer to buy again. You do that from the dropdown menu for the items on your orders list.
Or send them together anyway and change the tracking at View Order Details > Postage > Track Package > dropdown arrow. That has to be done on a desktop browser.
You don't need to refund for unused Simple Delivery postage labels. eBay automatically sends a refund to the buyer for any unused labels after 30 days.
Maybe the buyer is referring to business sellers who don't have to use SD and so can combine normally as before.