Sam,
I would continue to render the IR maps as you are doing. Once the IR map is done, just fix the areas in question. Unless you do any drastic moving of objects, you really do not need to re-render the IR map. The detail you'd get back from doing so, you'd probably would not notice. The same thing happens to me every now and then, and I never notice a big difference. Now if you are changing the color drastically (from grey to a bright red), you will want to re-render. But if it's just overlapping faces, I wouldn't worry about it.
As for how to render out animations... I highly recommened either rendering out from max in either .tga or .png. The reason being, if the render crashes, you can pick up from the frame it failed at. If you were to render a .mpeg out of max and it crashed, you would have to start from the beginning again. I normally compile my images in Adobe After Effects, but if Photoshop is working for you, then keep going for that. I'm sure there might be some cheap, or even free, video editing software out there that will take in image sequences.