BIAB change the current setting when the configuration does not correspond to what is set (for example by not finding the realtrack folder).
In my opinion, the user should be asked if he accepts the reparameterization, and above all, the new configuration should not be saved automatically.

This would make it possible to correct the pb outside BIAB then to relaunch BIAB with the initial configuration. This is also how most DAWs work (at least cakewalk)

Not only do we waste time configuring by hand and we lose the configuration of the plug-cs that often take time to configure