You see errors in your backup log which look something like this:
ERROR: File not found (System Error Code -43)
Deja Vu performs an initial scan which determines which files it needs to copy. If a given file can no longer be found when the time comes to actually copy it, an error similar to the one above will be generated.
Certain applications may make changes to the filesystem behind the scenes. You can often eliminate these types of errors by quitting applications and/or having your backups performed during periods of relative system inactivity.
If you believe these errors to be erroneous (i.e., the files in question have not actually been moved or deleted), you can also try this:
1. In the Finder, duplicate the folder(s) containing the files which give you these errors.
2. Move the original folder(s) to the Trash.
3. Rename the duplicate folder(s) with their original names.
4. Delete the destination folder(s) so everything will be copied again.
If you are backing up to a Windows share via SMB and see this error, you should consult this Apple Knowledge Base Article.