How to estimate Li Ion Battery SOC?
It is not entirely clear what you are getting at. What you SHOULD do if your model is detailed enough is periodically measure battery current and sum during charge and discharge to keep track of Amp-hours. Charge amp-hours and discharge amp-hours are very close to equal (very high Coulombic efficiency). The energy loss due to charge and discharge is mostly due to voltage differences. The voltage during discharge is lower than the voltage during charge, so even though the cumulative charge is the same, the energy is not.

The figures you are quoting may involve DC-DC converter losses or inverter losses. It is hard to tell from your question. But if the round-trip efficiency for the battery itself is 89%, that is probably due entirely to voltage difference. I don't really see how it can be apportioned between charge and discharge, nor do I see why it would be necessary to apportion it that way. Maybe it would be more clear if you provided more detail about your model. Maybe your battery model could just use an ideal battery with a small resistor in series.