You must measure your battery voltage per cell. If total voltage for 2S battery is only 3.7, that's like 1.85V per cell, your battery is totally dead. I am surprised you managed to charge it back.
Charging swollen battery you risk fire (or self injury if it explodes), pressure that builds up may damage the pack and if air mixes with the content you have fire. Also if you treat your batteries that bad, their internal resistance increase and they become harder to charge. With the increased resistance, charging them at the same rate accumulates heat which again might set a fire.
If you fly, and drain battery to 3.7V per cell, land, disconnect battery, it should jump back to 3.8V per cell, which is around perfect storage voltage (7.6V total voltage for 2S) given that your battery is balanced. If you drain your battery in flight to 3.6 per cell or lower it won't go back to 3.8 in rest, and you need to recharge them for storage.
Generally voltage per cell under load is different from the one in rest. Good voltage for storing is 3.8V in rest per cell, and battery should never have it's cells below that voltage for longer period. Flying to 3.7V per cell is ok, as good battery should jump back to 3.8 after disconnecting it, but it's always good to check and recharge if needed.
I use this
http://www.banggood.com/Wholesale-1S-8S-Li-po-Battery-Voltage-Tester-Checker-Indicator-Monitor-Buzzer-Alarm-p-26049.html which shows voltage per cell and beeps when battery gets low, but there are also other sensors or ways to prevent draining battery below safe voltage.