I've been working on scenery on my route for a couple of months now and have several large areas complete. About two weeks ago I unpacked the Donner Pass assets ".ap" file to access some .geopcdx files to get some repaints to work. Nothing seemed amiss with the route for a few days after. (Many of the scenery assets and buildings on my route are from the Donner Pass route)
The other day I revisited an area I had thought complete, and noticed that a large warehouse and some surrounding terrain painting was missing. (see below)

I thought it odd, but I just replaced the building with the same and moved along.
Today I've gone back to a forested area which was 90% complete to find several empty asset blocks, areas reset to 'default' terrain textures, and missing pieces from a trestle. The strange part is that the trestle which is made up of 2 assets repeated (trestle legs, trestle deck) has sections of both pieces showing, but others missing with milk bottles in their place.
If I understand correctly, the milk bottles should show up if Railworks can't find the asset to be displayed. Since the program has obviously located both of these assets, why wouldn't the rest of them in the trestle show up? (see below)

I tried loading a few previous backups of the route, but the same issue persists. What should my next course of action be? Verify Files? If so, what should I back up other than the route folder? Any help would be appreciated.