I have the exact same problem, but still haven't found any resolution to it. I've been working with Motion 5.0.5 (since the update came out) with all my files and projects on my system disk, never had the problem of missing layers. The problem started the other day, I decided to free up my system disk, I moved all my project files and elements to an external harddisk (Western Digital USB 3.0).
I'm assuming that the problem is not on the project file itself. I re-edited the same project, but again, layers started to go missing. So now I have two "bugged" projects which I need to reedit again. I can't say that the psd files layed in my motion project are the culprit because in the two projects that went "bugged" different layers/elements go missing (not necessarilly a psd file.
Will try to find a fix for this, i'll post immediately once I do (hopefully).