Just upgrade to Bitcoin Core 0.12.1. The upgrade will not mess with your wallet, and you will not need to redownload the blockchain. To be safe, you should backup the wallet file to a safe location. Just go to File > Backup Wallet and save the file to a safe place.
I think the problem is due to the way fees are calculated now due to network congestion. I'm not sure why the notice disappeared. I would recommend you backup your wallet, and upgrade to 0.12.1.
It has nothing to do with the fees. Please don't post if you don't know what you are talking about. The warning has to do with the CSV fork which is going to deploy soon.