eBay banned cash on collection a while ago (i'm assuming that's what's happened) so I don't think it's not possible now to manually mark as paid. The buyer is supposed to pay first via ebay and then they receive a code in an email and give it to you when they collect.
See "Proof of collection" on here:
https://www.ebay.co.uk/help/selling/posting-items/setting-postage-options/local-collection?id=4181
Doublecheck via Orders, select the item, and then More Actions dropdown arrow. If no luck you could try asking ebay to mark as collected. You can use callback on here:
https://www.ebay.co.uk/help/eua?id=5275&mkevt=1&mkpid
