Lithium batteries have two important voltages: Never charge them above 4.2 volts. Never discharge them below 3.2 volts. (For the sake of not confusing this I'll leave the 2.5 volt ok batteries out of this for now.) Charging the batteries over voltage or running them under voltage is when bad things start happening to Li-On battery chemistry, which results in internal breakdown of the battery, which can lead to accidents like battery vents.
If you have any APV - even the most basic eGo battery - they have protection circuits built in that shut the battery down when it hits 3.2 volts. You can't vape an eGo battery dead, you can only vape it until it shuts itself off at the safe low limit.
If you are using a mech mod there is no electronic circuit monitoring this. You have to pay attention to what is going on with your device and exercise care to not vape the batteries under voltage.
It sounds like you are confusing Li-On batteries with "rules" that used to apply to NiCad technology, and to a much lesser degree NiMh batteries. That's not what we are using here. There is no penalty if you put a partially discharged Li-On battery on a charger. They don't have a memory effect like NiCad does, and it neither shortens their overall life span or run times. And you never want to fully drain any Li-On battery - that's one of the worst things you could do to it.