1) I noticed that if files are uploaded to a directory outside of b2evolution Filemanager that they do not appear in the $FileCache/File list even though they are visible in the File Manager.
2) Does b2 not scan media files directories for changes?
3) Is there a way that b2 can rescan media files directories to add files to the database that were added outside of the File Manager?
b2evo never scans directories. Files are added to the DB only when they are needed in the DB; for example: when additional properties are added to the file or when it is linked to a post.