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I'm going to start by saying this is an "emergency", because the delivery of my new battery cells are delayed.

I have two 3S Li-ion batteries: one with 2250 mAh (50 C) and the other with 3700 mAh (35 C). My load is an RC plane DC motor, that draws around 50 A at full throttle (it stays at full during the takeoff, for around 3~5 seconds). The total time of flight is supported by both batteries (with a reasonable safe margin, and using 50 A for the calculation).

Is it safe to use, only a limited amount of times and without dangerously discharging, these two battery packs in series, even with the different capacity?

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The fact that they have different capacity would not be a problem if the cells were protected by a single protector BMS.

The problem is connecting the two batteries in series, regardless of whether or not their capacity is the same.

  • If the two batteries include a protector BMS, then the problem is that, when the smallest battery shuts down under load, the entire voltage of both batteries (about 20 V) appears across its transistors and they not be rated for it, blowing them.
  • If the two batteries do not have a protector BMS, then some cells will be over-discharged and the next time they are charged they may catch on fire.

So, in either case, what you're doing is dangerous.

Regardless, connecting the two batteries in series doubles the voltage to up to 33.6 V. If your toy expects a single 3S battery, connecting to two batteries will blow it up.

The only safe solution is to use a single battery of the correct voltage with a properly installed protector BMS.

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It is a bad idea and dangerous. One of three things will happen: two, you will not like, and the third, you may not care much about it.

Your motor and controller better be 6S. You mentioned 3S packs, indicating your equipment might be 3S. Apply 6S to a 3S system, and you will let the FM smoke out at takeoff or during flight. Gravity and smoke take over aircraft.

You run a very high risk of over-discharging the 2200 mah battery. RC Lipo batteries do not have any BMS built into them, it would take up too much weight and space in an electric aircraft. The over-discharge goes directly into reverse polarity, thermal runaway, Twist & Turn—Crash & Burn.

Last but not least, if the motor and ESC are rated for 6S and you do not over-discharge the batteries, you might get away with it. If the motor is 6S, you could bottom-balance the packs. Fully discharge both batteries and recharge to 2200 mah. That eliminates the over-discharge.

Get the right battery.

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