Chief still doesn’t allow Auto Rebuild Foundation to stay on once you draw interior walls in the basement. As soon as you add manual walls on the foundation level, Auto Foundation turns off because a rebuild would delete anything you drew manually.
Right now the only workaround is to keep Auto Foundation off and use Reference Display + Align w/ Above/Below when the main floor changes. Otherwise you can copy the interior walls, rebuild, then paste-hold-position.
If you want this behavior changed, it really needs to go in as a feature request to Chief.