Atropsiomer detection is not part of the usual assignStereochemistry() workflow. This means that Atropisomers will only be detected at import time, or when an explicit call to detectAtropisomerChirality() is made.

This means that atropisomers won't be detected, updated or cleared (since assignStereochemistry(cleanIt=true) also does not clear atropisomer bond stereo markers either) after that, even if we made changes to the mol that directly affect the atropisomer groups (e.g. reverting the bond/parity that defines the atropisomer), leaving the mol with invalid stereo.

It feels like the atropisomer detection should be triggered inside assignStereochemistry().