Quote

How exactly did you do this? Did you shutdown Bitcoin Core, move (not copy) the original wallet.dat file, and then start Bitcoin Core?

Before opening Bitcoin Core, I backed up my everyday wallet. I then deleted the copy of wallet.dat in the Bitcoin folder.
I then opened Bitcoin Core, it behaved as expected, it had a brand new looking wallet, with no bitcoin and no transaction history.
I then used importprivkey ############### "MyVanityNickname" in console. It took like 30 min to rescan.
I could not see any address in the address book, which I thought was weird, but as it had no bitcoin and no transactions, I thought maybe it might just not show up
So I shut down Bitcoin Core. I backed up this new Wallet.dat file, then I copied over my existing wallet.dat file to the Bitcoin folder. Computer says " Do you want to replace the existing wallet.dat" and I say yes.
I fire up Bitcoin Core. It is my old existing wallet as expected, with my bitcoin, and my transactions. To test that the import happened correctly, i send a tiny amount of bitcoin to the Vanity public address.
Transaction history now shows I sent a transaction to myself, and "MyVanityNickname" is in my address book. This I found very weird.
I shut down, backed up again, moved the new wallet.dat back into bitcoin folder (ie the empty one I imported priv key into), fire it up.
New wallet.dat shows the tiny balance I just sent it, but nothing else.
I power it down, swap wallet.dat files again, fire up my old wallet. It shows the tiny amount being sent to myself. To test I then select input coin control, to see if I can send tiny amount to my mobile wallet. ( ie see if my old wallet does actually have the private key to that address)
Bitcoin are sent to my mobile successfully.

Quote

It would appear that you've either imported that private key before (have you previously used vanitygen?)... or you hadn't actually opened Bitcoin Core with a "new" wallet.dat and you actually imported the private key into your "original" wallet.dat

Nope neither of those things I don't think. Definitely had not imported it before. The new wallet was generated because their was no wallet.dat in the bitcoin folder