"The best way to import your AE comps is to export from AE to AME, using Command Option/Alt + M or going to the top menu, Composition > Add to AME Queue. Some things to note with this method:" Yes, that's what I'm doing. I change things in AE to reflect what I want the final output to look like, eg. show/hide my clip layers, adjustment layers, etc. I then go to File->Add to AME queue . It appears to send it, but when I go to AME and try to use the "export settings" dialog to adjust the output length, it shows me whatever the first queued job is. So, once a job is done, I delete the job from AME, quit AME, go to the render directory and clear the temp file, go back to AE, adjust things for the next render job, and then "Add to AME queue" again. I go back to AME once it opens, adjust the length of the now correct clip and render. Maybe I'll restart my system and see if some magic happens.
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