eBay won't help if it's more than 30 days, as you know.    Also if it was returned outside of the ebay system.   

Persevere with your bank or try the small claims court, now called money claim online:
https://www.moneyclaim.gov.uk/web/mcol/welcome

Also contact Trading Standards about the seller. 

eBay's money back guarantee applies in the same way to large corporate sellers as to small sellers.

So does the 30 day time limit to open a case. From what you have told us it sounds as though you may not have opened one? If not, it will be too late now.

As a bank chargeback isn't available in this case you may just have to resolve this with the seller yourself. It's difficult to offer suggestions as we don't know what happenned. You could speak with Citizens Advice, or if there's enough money involved consult a solicitor.

So this was a change of mind return and you used the seller's return system, within the legally required timeframe, to return the item?

Not providing a VAT invoice is not a case for a not as described return.  And the seller only legally has to provide one to another business.

The VAT invoice was stated to be provided in the original listing, the purchase was by a business. The Seller accepted the fact they had mislisted, and accepted the return not via eBay (they sent a label) as it was beyond the 30 day window to open with eBay.

Thanks for advice above, I am going to push for a Section 75 Chargeback which was the advice from CA. But will move to a more legal route if necessary.