We're experiencing an issue wherein one of our image assigned app layers is somehow dropping a file when we publish the image template, assign the .vhd to a server in PVS, and restart said server(s). We use the same app layer in a different ELM, from which we export the layer and import into the faulty ELM, and the file is always present in the resulting PVS target. We've mounted the faulty .vhd on the PVS server and the file that has gone missing on the targets is present in the .vhd.

Are you using elastic layering on that image? That could affect what a user sees if that file was somehow deleted in an elastic layer.