but shouldn't I just get a polite "that piece of footage is no good", the ol' test-pattern, and be able to keep working and come back to it when it's ready?
In theory yes, but as I just explained in another thread, 64bit AE vs. ye olde QT is full of workarounds and limitations due to Apple not seeming to care at all. That and the differences in 64bit file access on a more general level may lead AE to wrong conclusions. I'm sure it's a bug of sorts plus perhaps your 3D app (Cinema 4D?) could also do better by closing and re-opening the file from time to time so at least some parts are accessible instead of keeping it permanently open. For the time being, simply use image sequences...
I had this "Zero denominator comparing ratios" issue in AE CS6 when puppeting an AI file. The file was imported as a comp with an odd screen ratio, and was being used with the puppet tool to create a character. When I changed the artwork and reloaded the footage, the mesh would not match and this same error arose. My solution was to quit and restart after effects, so the footage would load, and then initialize a new puppet pin, creating a new instance of the puppet effect. I was then able to copy and paste my pins and expressions from the other puppet effect and the character was back to life.
Note that if your mesh resolution settings are any different your pins may move!
I just had the "After Effects error: zero denominator in ratio addition. (17 :: 16 )" while trying to RAM Preview a composition and a quick solution that worked for me was switching my Fast Previews from "Fast Draft" (which I was working in) to "Off (Finest Quality)". I was then able to RAM Preview the entire composition.