In Darktable, the practical way to refresh a folder tree is to import the same root folder again. Darktable will skip images that are already in its database and add any new ones it finds.

Based on the community answer, there isn’t a built-in automated rescan/sync process for watching a folder tree and updating it automatically. So if you add files or new subfolders, re-importing the root is the safe manual method.

For deletions, catalog-based apps like Darktable may still show entries until the missing files are detected or cleaned up, so the main takeaway here is: re-import to find additions; automatic syncing is not available.