The intended workflow is to only use Autogenerate once you are fairly sure most lights are in your scene, and only make production changes to LightMix values once you are also sure that most lights are in there; then when smaller changes are made to lights in the scene (additions, deletions) LightMix can then be manually updated as that is easy to do for just a few lights, adding them to existing LightSelects or creating new ones. Reusing autogenerate will indeed overwrite values etc. so if still making major changes to the lights in the scene, best to avoid doing anything precise and final with the LightMix settings.
Another option if you do make production final tweaks to lights before finalizing the lighting in the scene, is to bake those values back into the scene, then you can use autogenerate again, and your previous changes were transferred from LightMix to the pre-existing lights.
We have it noted that some folks may want to do otherwise than these workflows, but there's no timeframe on if and when we might revisit that, sorry.
