Can you connect in series 2 unequally charged batteries?
This sounds like a bad idea. Besides the fact that it says not to do this on the battery package, here is the reason:







simulate this circuit &ndash; Schematic created using CircuitLab

As you can see, the batteries that are used have a lower cell voltage, but also a higher internal resistance. They aren't contributing much to the power delivery, and they will dissipate quite a lot in heat! This will eventually rupture the battery.

Your bypass might work if the circuit is capable of using a lower voltage, and the batteries you use are capable of delivering a higher current to compensate for the reduced voltage.