I didn't find any fixes but the one workaround I did was to keep re-opening my project until it looked like all the layers were present and then to split the project timeline into two smaller chunks. This allowed me to actually continue drag-and-dropping content as per normal, which made me think this could have been some kind of memory issue.
One downside is that I had to join the pieces together and encode using FCP which added an extra process.
Regarding the dissappearing layers, I had a feeling that it started happening if I directly edited and re-saved PNG content in Photoshop while it was linked and open in the Motion timeline. I enjoyed watching the live 'flick' of the graphic updating but now I'm too worried to do that.
Hope this helps alleviate some crazy.