Metadata issues after a restore of drive with acronis on it

Hi,
Acronis is installed on my OS partition of my Win 7x64 system. I run nightly differential backups with a full backup every 4 days of this partition and some others.
I use a batch file triggered post-backup to run a second backup to my NAS and then shut all of my systems down.
In the even I have had to do a restore and overwrite the OS partition I find my backups are then messed up and kick up an error. The NAS backup does not then run.
I think this is because the metadata is being over-written on the restore?
How do Iget around this or what do I need to do once I conduct a restore to ensure both backup schemes continue as normal?
I considered just editing and saving as a new scheme, deleting the old settings but wasn't sure if that was optimal.

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