I assume when you run the
feature_extractor on the same images it overwrites the custom features you already added?
I don't know what happens when you run one of the feature matchers using features that lack a descriptor -- I would avoid that.
You could run the feature_extractor first and then run one of the matchers (e.g. exhaustive_matcher) . After both of those are finished then you
could add your custom features and matches to the DB. If you know the camera model and parameters you can add those to the DB at the very beginning
and make sure to specify --ImageReader.existing_camera_id for the feature_extractor.