It looks like you have sorted out the problem yourself. It seems that using the schnorkel for recharging was also the historical procedure:
http://www.uboatarchive.net/BDUOrder1.htm
According to BdU's orders schnorkeling was to be done in conditions unsuitable for airplanes, when possible.
Anyways I'm glad I now know what to do with the schnorkel, if I get it one day
