3V per cell is the bare minimum and I would try stay away from that as much as possible as some ESC can shut down at 3V and cause a crash ! I think that 3.5V is ok, it will give you about 60 seconds or so land which should be fine but some people push it to 3.4, or 3.3v! I guess it really depends how far you plan to fly. I think it would be cool to calculate this low voltage fail-safe based on the distance from home, maybe ina future arducopter release :-).
One thing that I would highly suggest is that you make sure that the APM power module is calibrated properly.
Calibrate APM power module
First check if it needs calibration
- Check the voltage of your lipo battery with a hand-held volt meter or a power analyzer
- Connect your APM/PX4 to your computer and plug in the lipo battery
- Check the voltage through the mission planner’s INITIAL SETUP > Optional Hardware > Battery Monitor screen or on the Flight Data screen’s HUD or Status tab.
If it needs to be calibrated then do the following.
- Go to the battery monitor screen (under initial setup>optional hardware)
- Enter the voltage according to the hand-held volt meter in the “Measured Battery Voltage” field
- Press tab or click out of the field and the “Voltage Divider (Calced)” value will update and the “Battery voltage (Calced)” should now equal the measured voltage