Unless something is wrong with the switch on the jack, there shouldn't be a circuit between the jack and the battery while you're cranking it manually, it would be open at the switch. I can't see how manually operating the jack would affect the charge of your batteries.
Zero Gravitas — 2017 Flying Cloud 26U | Il Progetto — 1976 Argosy 28 Center Bath | WBCCI# 15566
He has all of the virtues I dislike and none of the vices I admire. — Sir Winston Churchill