Eccentric Butterfly:
When I go to backup my Qubes, the backup screen shows a red error at the bottom of the 
window saying "Warning: unrecognized data found in configuration files".

Try closing backup, then "rm /etc/qubes/backup/qubes-manager-backup.conf" in dom0 terminal. This will delete the configuration you saved last time you ran backup.

Why is this? Is there anything I need to do? Will this have any effect on my 
ability to backup and restore?

Haven't seen it before so don't know if it would prevent backups or restores.

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