...and I'm back in the game!
In the English rules, it says:
It is possible that a resource board contains more than 6 disks. In this rare case, the final resource board that has to be supplemented will get less than 6 disks.
We usually refill pools top to bottom, even though the rules don't specify which to fill first.
Side note: I'd have to agree that it is rare for this to happen. I think I've seen it happen once in 20 plays.