Versions of BibDesk prior to 1.3.13 stored links to files as paths or a file: URL. File links are now stored as a relative path (relative to the .bib file), and as a Mac OS alias. This allows AutoFile to operate on an arbitrary number of files, and allows you to move your files in the Finder without breaking the links in your database. But when you do, you should alsways be careful, check the database and make sure it is saved.
When you open a file that has URL fields (Local File and Remote URL fields), they are automatically converted to aliases (or paths, if the file can't be found). When you save the file, the new information will be saved and will be used exclusively the next time that file is opened.
The new file fields will appear as `Bdsk-File-N' in a text editor, where N is a positive nonzero integer. They are not human readable, but can be accessed via AppleScript and Script Hooks. The new URL fields will appear as `Bdsk-Url-N' in a text editor, and are human-readable.
The "Convert File and URL Fields" item of the "Database" menu allows you to see which files could not be found, and to clear out the old file and URL fields such as Local-Url and Url. Changes are undoable, but you may wish to make a backup of your file before proceeding.
"Convert File and URL Fields" mimics the automatic conversion performed when first opening a file that does not use the new Bdsk-File scheme. The primary difference is that the manual process is more flexible and displays warnings. It can be run at any time, even after a previous manual conversion.