Maybe the balloon could condense water in its environment and electrolyze it to refill itself with the produced hydrogen. (Though I'm pretty sure you also need salt.)
If a balloon is relatively small, and designed never to come down, would it be such a bad idea to use hydrogen as the lifting gas? We're understandably a little gunshy about using hydrogen after the Hindenburg, but surely we could come up with some safer designs now.
Hydrogen is a great lifting gas, but because the molecule is so small, it leaks out easily.
There is very little water in the air at those altitudes. Also, electrolysis uses a lot of energy.