Acquiring and maintaining an accurate value for the gain difference is arguably one of the most tricky parts of the whole operation. Even when using two parts of a stereo ADC so at least the Vref is tied together, there is always going to be a small amount of gain drift due to different tempco and aging in gain-determining resistors in external circuitry. Not to mention there might be tiny differences in frequency response as external analog gain differs.With actual ADCs there are more errors and inconsistencies to deal with.
Ideally what you want is an algorithm that is continuously monitoring the output of both ADCs as long as neither is clipping and both are well above their respective noise floors. Starting at a built-in preset value, it would perform sort of a moving average ideally stretching over minutes. And that's only after you've EQ'd out the FR differences, hope that those are static enough at least.