Brian,
I double-checked with our development team and you are absolutely right. The favorites do not currently get stored as part of the backups.
This is left over from an earlier design, which made a distinction between user interface customizations vs. 'actual' data.
We will look into changing this behavior for upcoming major releases.
I have also double-checked that this is the only information that is not backed up. (Of course license codes aren't 'backed up', since that would pose a licensing issue...
)
Thanks for bringing this to our attention!
Support Team