I have a laptop with a docking station, a home environment with two external monitors and a work environment with two different external monitors. I also use Display Fusion. In all cases I have the devices setup from left to right, displays 1 to 3: laptop, monitor 1, monitor 2.
The snapshots I had taken for the work environment appear to restore correctly only momentarily before swapping to incorrect monitors. Looking at the XML for the snapshot it appears the goal of the process for restoring the snapshot is to overwrite registry values. When I look at the registry values in RegEdit it does not appear these changes are sticking.
I was able to get my snapshots to eventually stick when fiddling with the Windows 10 Immersive Settings App's Display Settings.
At home my laptop screen (display 1) is my 'main display' as the Settings app calls it. Display Fusion calls it the 'Primary Display' in it's Monitor Configurations window.
At work my left external monitor (display 2) is my 'main display'. I believe the original goal of this change had been to get the icons and fences that would display at home on my laptop screen to instead display on display 2 at work. This hasn't worked too well and I tried to make a couple of snapshots for each environment.
In all cases the right external monitor is display 3.
When trying to restore a snapshot with display 2 as my main/primary display I get momentarily correct layout/fences-to-display assignment.
If I tell Windows to designate display 1 as main/primary and restore the snapshot everything is as desired. It is not apparent if the DisplayFusion and Windows Settings always line up in agreement of which display is main/primary.
So it seems like snapshot recording and restoring works consistently as expected only if the main/primary display is always consistent (perhaps with display 1 always being main).
AzDude or Rohan, let me know what questions you may have.