Vybrid Colibri VF50 - clone the sytem

Dear Toradex Support,

I am asking for a little guidance how to fully clone a VF50 card.
It has bootloader: 4.3, image (ce6): 4.1, update tool 4.1.0
Because there are situation when the module got damaged and I have to restore it to another one.
What should I save from it and how?
I mean I save the flashdisk of course, and with the update tool the registry. What else should I save?

My issue is If I save the registry and flashdisk the windows certificates damaged or not restored properly.
After I do a flashdisk and registry restore I can see the certificates in Control Panel / Certificates / My Certificates, however our software cant work with it anymore.

Thanks for you help,