My Phantom is at the factory for? probably 6 weeks and both of my batteries are fully charged. Is it going to hurt them to remain charged for that long? and if so is there a way to discharge them without my phantom? What happens if you just turn them on out of the phantom?

it will stay on for 10' i think, and then it will auto switch off.
it will take you alot of hours to discharging with this way.

The batteries are smart batteries. After 10 days they will discharge themselves down to 50% . It will take them a little while to discharge but they will . Just put them in a safe place that you would for any lipo. There are a lot of  discussion as to safety of lipos. Some store them in ammo cans. Others in fireproof lock boxes. I just keep mine on a glass top table, nothing close by that could burn in case one of them erupted.  There are a lot of video on you tube about lipo safety.  Hope you get you bird back in less than 9 weeks. Take care!

Newer battery FW versions have the auto discharge after 10 day features,  older batteries without the FW update do not have that feature.
No issue with switching the battery ON outside of the Phantom but that alone won't discharge them.  A simple way of discharging them is to use an automotive incandescent light bulb ( 20 Watts or so) and a socket for that light bulb with wires.

PanamonCreel Posted at 2015-5-28 21:31
Newer battery FW versions have the auto discharge after 10 day features,  older batteries without th ...

thanks for the info!