After performing a backup with the 'Remote backup' option checked, you find that not all of your files have been copied to the destination folder as expected. Additionally, you notice a line resembling this one near the beginning of the backup log:
Using /Users/you/Documents/.psync.db to retrieve extra attributes.
The above line indicates that Deja Vu is operating in "remote restore mode". If you ever swap (reverse) the source and destination folders in Deja Vu, this problem can arise.
Delete the file which is keeping you in restore mode. Enter the following command in a Terminal window (changing the path as appropriate):
After doing this, always backup in the same direction (unless you are specifically restoring files to an empty destination). Understand that Deja Vu considers the destination folder to be a backup of the source folder, and nothing more. In other words, it expects that changes will only be made within the source folder, and not within the destination folder.
If you are not backing up over a network, then 'Remote backup' should not be checked, and the above no longer applies.