I received some more, but not all. It does seem to be fixed now. I'm guessing it won't be possible to "fix" it completely if mining was carried out on two forks, not without a time machine

Some of the mined coins will simply cease to exist.
Well, it kind of sucks to lose the coins for 2 full days of mining. I'll just chock it up to a life lesson and use the auto pay feature at all pools I deal with to minimize the loss if something like this happens again.
It wouldn't have made a difference. Remember the "coins" only exist in your wallet because they show up on the blockchain. It isn't like a bank account where money is transferred into it. So when a fork happens, and then gets resolved, any transfers done and new coins created on the fork that didn't survive don't exist. It's like they simply never happened at all. So if you have done auto-payout, once the fork was resolved there would be no record of your payment on the blockchain and no record those coins were ever created in the first place. Your wallet, once it updated to the correct block chain, would show the lower balance without the non-existent coins.