@martindeveloper & @briandanimal, what versions of Duplicati are you using?
While this is a valid issue (and not yet “fixed” as far as I know) it’s possible this is not what’s happening in this case.
I say this because I, too, ran into a single machine where the configs just disappeared - and there was no Windows.old folder.
In my case it was with version 2.0.3.6 but the machine was not in my direct supervision so I don’t know what had been done to it in the 5 weeks since I had last seen it. I’ll try to do some forensics on it to see there’s a Windows Update history that coincides with the last write date to the .sqlite files…