It's unlikely they're toast, just keep a good eye on them on the first run, or use the "discharge" or cycle function on your charger, also keeping a close eye on them. 3 months isn't that long.

As for storage, If your charger has a "storage" function, this will bring them down to 7.6 volts (for a 2 cell) which is said to be a safe storage voltage. Many racers I know also put them in the fridge after bringing them down to 7.6v. (ask the wife first). From what I hear, this is like hibernation for the batts.

I'm no expert, but that's what I do.