unless you turned the battery disconnect switch off when stored, a single 12V battery will discharge in a week or less. Why?? well first off, the radio in the OFF position is really in STANDBY and draws about 0.3A, thats about 8AH/day, 7 days = 56AH, half or more of the battery capacity. couple with a few other parasitic drains, and yup, battery goes flat quick in storage.
turning off the breakers does NOTHING for battery drain. The breakers are ONLY for the 120V circuits. All the 12V circuits are protected either by fuses or Circuit breakers in the 12V panel.
And, the 400W generator, probably will overload trying to power the charger. The charger will draw more power than that easily. Unless the generator has a 12V DC output capability.
if you don't have a battery disconnect switch, then unhook the battery positive cable whenever you store the trailer.
Even two 6V batteries would have been drained heavily after 3 weeks, although they would likely have slowly worked the jack and awning.