At about 12.30 my Post Office received an Email from Royal Mail, telling them to accept the 48 tracked post with the dodgy YB tracking numbers.
They scanned all my items into the system, they just couldn't give me a proof of postage. I use Click and Drop.
The issue has nothing to do with Ebay (although it has a knock on effect) or SD, it is a Royal Mail systems issue.
I've just checked on my Click and Drop account and all items are now showing as received by Royal Mail.