You can take multiple exposures of every frame, I have done shots where I shoot one exposure with the object and the flying rig and then remove the object for the second exposure, it will put them in different folders. You just need to make sure to turn off automatic second exposure frame capture otherwise when you capture the frame it will take both pictures without the option to remove the objects from the frame.

This will of coarse require you to remove and replace whatever you are animating every shot which can be a pain, so if the shot is static and does not have camera moves it might still be easier to take black frames and the beginning or end.