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.