I’ve been exporting extremely large videos to allow for HD zooms in After Effects, and I’ve found that past a certain size, the output is scrambled and unusable, whereas the smaller versions are fine. The larger sizes I’m trying are around 6000 pixels on one side, and those are unusable. It seems like about double 1080 resolution is about as high as I can go before it gets bad. I’m exporting to animation high quality quicktime files.
You should output as a sequence of images instead of a compressed movie for best quality.
I’m exporting the audio as well - it’s annoying to have to re-sync the audio to the lip sync outside of Toonboom, since I’m dealing with a large amount of dialogue clips. Seems like many people would be exporting large files, but I guess not.
A lot of people prefer to make the final sound edit in the editing suite also because the sound that you will get from a compressed QuickTime will be modified from the original. It depends on the quality needed I guess.
An Automator action to flatten every movie Quicktime is able to open. It does so by invoking the Quicktime.framework. Without opening Quicktime, the advantage is that no Quicktime window floats around, which can obstruct your desktop.
The use is straightforward. You need at least a Get Specified Finder Items, select the movies you like to flatten. Plug the Flatten Movie action after it, choose the destination. 
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