What I'm asking is if there is any loss in fidelity if I take an AE project, render it as a lossless file, then bring the file back into a new AE project.
What Mylenium and Rick say is right, but there is one important thing to ask when someone says that a codec is "lossless". Some people abuse that term to mean "perceptually lossless"---i.e., a human can't tell the difference. When you think that someone might be misusing the term this way, always ask if they mean "perceptually lossless" (which is actually lossy) or "mathematically lossless".
A couple of examples of mathematically lossless codecs are PNG (at highest quality) and Animation, both of which can be used as video codecs in a QuickTime container.
Why does the distinction for perceptually lossless matter? Because much of the information that computers use for things like motion tracking and color keying is exactly the information that humans can't distinguish---so a perceptually lossless codec can actually wreck a video for compositing purposes.
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