Backup Messages and Restore

I’m trying to implement a Mobile Device Management software. The phones we have must be put into supervised mode which requires a factory restore. Once i get the phone into supervised mode i cannot restore from backup because it seems to un-do the supervising.

How would i backup and restore iMessages & Address book without using iTunes / iCloud to do a backup

The product i’m using is Cisco Systems Manager for what its worth. I have Reincubate iPhone Backup Extractor but I don’t’ see a way to re-import the extracted data.