I also am mystified by this talk of a "content file". What file extension do these content files have? Is this a static scene or an animation?

I use P6 and when I save a scene I only get a pz3 file, unless "Use external binary morph targets" is used, and I recommend  not using that option.

The problem sounds a lot like the pz3 files are getting corrupted on save. I have had that happen on the very odd occasion, but it should not happen on a regular basis. Perhaps the cr2 for figure you are using (or some other item in the scene) is corrupt, and this is causing a problem with any scenes it is used in. That is the only thing I can think of of the top of my head.