Disappearing Frames

I saved my project that I plan to use later as my demo reel, but when I exported it, a big chunk of frames had disappeared and I don’t know how to recover them. I don’t know if this helps, but I drew my characters in red and blue; so I’m thinking it may be related. For future reference, do I prevent this from happening if I render my animations in black ?

Your line art can be any color. Did you ever figure this out? If not, are there more details or screen shots that you could add here to show the problem.