To reset Darktable’s databases, delete the two databases (files ending in “.db”) in the equivalent to ~/.config/darktable on your Mac.
One contains your custom configurations like presets, the other contains info about file locations, ratings, film rolls, etc.
Deleting and reimport takes time when a lot of files are involved, but is my preferred way of handling the changes of large scale file operations.
But film rolls might not be the best way to manage files.
After six years, I found searching the database using tags and Exif data such as camera and date ranges with the collection tool works better for me.
What also helps me is never deleting or moving an image file.
That way the database stays current and I avoid the busy work of file and folder manager.
To put it another way, for me flat search is better than hierarchy navigation.