MSL backups will only store the MSL config data. To backup the NuPoint config and messages you have to enter the NuPoint text console and run either a USP or LAN backup in NuPoint.
I've done full restores of MAS/MiCollab systems and had the NuPoint data transfer. Standalone NuPoint used to require two seperate backup and restores, but MAS/MiCollab has been doing this for a while.
I would point you to the release notes of NuPoint 8.1 for this:
"After you upgrade NuPoint UM software on a standalone VMware platform, the system will automatically restore the software blades and NuPoint database. Previously, these steps had to be performed manually."