Nate :We have fixed a similar looking problem in 3.8.87 which may also fix this for your project. We should release that in a day or two. Until then, you can try never opening the export preview, which may workaround the problem.
Apologies for not sending in the project, I've been real sick and out of commission.
Not opening the preview indeed fixed the issue for the missing meshes but it still doesn't export the whole animation - it seems to abruptly cut it for MOV export specifically. The animation is 2 seconds long at 60fps.
I'll wait for the next update, if the issue still persists after that, I'll send in the project.