I wouldn't recommend putting a 3700mah and 4400mah lipo cells in series.
As soon as the motor starts drawing current the cells will immediately become out of balance. The voltage of the 3700mah will drop faster than the 4400mah battery.
Let's say your low voltage cut-off is set at 6volts. When the voltage of the combined cells in series reaches 6volts, the voltage of the 3700mah cell will be below 3 volts and the voltage of the 4400mah will be above 3 volts.
This will damage the 3700mah cell.
If you connected balancing leads of the 3700mah to some sort of low voltage audible alarm to make sure that you do not go below 3 volts then it may be OK.
But in general, I wouldn't recommend mixing two different capacities packs.