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Depends on the method used, I guess. Interlaced and side-by side should be no problem beyond the fact that they reduce resolution. I would also think that they had a ton of scripts, expressions and possibly even their own plug-ins. In any case, you can't preview in AE, so they most definitely used custom software for that as well. Blackmagic is offering something for Premiere together with their cards...
Have you seen any documentation on working with AE in stereo? I'd like to read it. I have a pretty good idea of how to pull this off, but if people are already doing this I'd like to see their workflow if possible.
Thanks Todd! Great stuff!