Looking for guidance - battery reconditioning

The important number is the discharge mAh. That tells you how much energy the module is actually storing. I always assume about an 85% efficiency for charging if the module is in good condition.

The initial discharge will always be a bit low, since the car maintains only a 42-65% state of charge. Each module is rated for 6500mAh when new. A 42% state of charge would only be around 27-2800mAh. 65% would be around 42-4300 mAh. So if you're getting ~3000 on the first discharge, that's pretty normal.

 

The charger merely measures how much energy it has sent to the load (module in our case) as electrical energy. In your case, it's set up to stop at 6500mAh.

There's a couple things going on at the same time.

One is battery charge efficiency. A module in good condition should convert around 85% or better of that electrical energy into chemical energy. The remaining electrical energy is lost due to inefficiencies like heat, etc.

Two, the module may be in a condition where it can only store 3000mAh worth of energy. In that case, the charger should stop charging when it detects delta peak voltage, or at 6500. If it reaches 6500, that means: about 3530mAh went toward charging the battery (3530x 85% = 3000mAh) and everything after 3530 (the remaining electrical energy) was just converted to heat in the module.

I'm not sure if I explained that very well.

You can pound 6500 mAh of energy into each module. You can also pound 10,000 mAh of energy into each module.
Every module is slightly different and each module is only going to charge as high as it's chemicals will allow, whether it's 1000, 2000, 3000, 4000 or 6000. Once it's chemicals are at "max storage" any further electrical energy pushed into it is just being converted to heat.

We then discharge it and measure how much energy "the chemicals" release back to the world as electrical energy. This is the number that matters, since it is telling you how much energy that module can hold. Typically, as additional cycles are performed, capacity increases up to a point where it levels out.