I'm jumping in a bit late here - but this same issue JUST happened to me.
New computer purchased in January so everything installed fresh. I am running P3D4.2 on Win 10. All of my PMDG aircraft are fine in the sim. They are suddenly all missing from the Ops Center EXACTLY as described by the OP.
I checked each PMDG aircraft individually to verify they are not in the Ops Center. I also have never run the Ops Center as admin and it has always worked. I agree that something has changed either through a Win update OR the wonderful Support Assist program pre-installed by Dell on Alienware machines. I'm thinking that it's 'optimization' process must have deleted a registry setting or file that the Ops Center uses to 'see' the sim.
So - PMDG is there a particular reg setting or file used by the Ops Center that I should check for?
Thanks,
Keith Lovell