You should never let a Lipo battery discharge below 2.5 volts per cell absolute minimum, 3 volts per cell is a safer limit. Normally you should aim for running to about 80% usage, so for a 5000 mAh battery you could use 4000 mAh. This will prolong the life of the pack and also give you a reserve in case of problems, especially useful for a multicopter.
It's also a very good idea to always balance charge the packs, it will again prolong the pack life, and give you early warning of a faulty pack.
pca
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Experience is what you get just after it would have helped...