There is nothing in your title to say the box had been opened. The item specifics state it's brand new factory sealed. Your description states that the item was meant to stay in the vault. That does NOT tell me the item has been opened. There is absolutely nothing in your listing to say the item has been opened. 

Personally, for $999, I'd be sending a postage label and get the item back. Unless of course the buyer is happy to accept a part refund (as a collector of items nothing like this, if I bought what I thought was unopened and it wasn't, I'd want at least 50% back because the second it's removed from the box, the value plummets). 

Accept the return, give a full refund and relist as the item should be. If you don't accept the return, the buyer will ask ebay to step in and help, which will mean you lose both the item and the money. Ebay will nearly always side with the buyer, and definitely will in this case. If you don't accept the return and the case closes, you then also gain a defect on your account, which means your listings will go waaaaaaay down, and in some cases, may not be visible at all.

Just another note.

These are expensive and highly collectable items (not sure why), and ways have being found to open and determine what is in the package.

The seller even muddies the waters in their description.

Also take a look at the sellers feedback left for others, and they complain about exactly the same situation, 

The 'no returns' is change of mind only

If the buyer opens an item not as described dispute, the no returns is not going to cancel that out for a second

No, you don't have a leg to stand on in eBay's eyes

eBay are not going to take into account 'an oversight'

It even sellers on listings 'sellers are responsible' for said listing

The buyer may not have even read the description (many don't bother to), they could be taking advantage of said oversight who knows 

I don't actually know which item it was where this happened. I had a look at your 'sold' items & the only one I can see where you stipulated the item was used in the title was one that sold at $269, but it also said opened in the item specifics. So I don't know.

However, I can feel your pain if you did clearly specify opened in a title and description, and the only place it said new/unopened was item specifics.

You'd think any buyer who came across this discrepancy would ask you before buying but in reality, some buyers don't read the ads carefully.

I think, because of the contradictory nature of the listing, you should probably accept a return with a refund to be made upon return.

The other thing you could do, as someone else mentioned, is offer a partial refund.  Explain to the buyer it was an oversight, but also mention that the word 'opened' (or whatever term you used) was in the title and description. You need to acknowledge responsibility, apologise and ask if they would prefer to return for a full refund or accept a partial refund.

As I said, I can't tell which ad this is about but in titles, I would steer clear of saying anything such as 'Not new/factory sealed'. Instead say 'opened' or unsealed. People often just glimpse at things and might miss the word 'not'.

Many buyers will not see the full description, particularly if they are using the eBay app.

The item specific that stated “new/factory sealed” trumps your disclaimer in the description. (Even if it did not, the contradiction is your responsibility, not the buyer’s.)

No returns only applies to change of mind returns. Surely you’re aware that buyers have a right to return/be refunded when an item is not as described. Furthermore, the return postage is also your responsibility.

You can offer a full refund upon return (you’ll need to provide return postage label as per the MBG), or you can offer a partial refund if the buyer is willing to accept that, or you can refund without the need for buyer to return. Those are your choices.

Sorry reading the ad I would assume new in sealed pak,  you openly admit here it isnt.  Refund as it is not a described.

Also you cant say no returns or refunds if the item is defective or not as described.

Valid complaint from the buyer,  not their fault you listed it incorrectly.

Do the right thing