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How do I transfer files from Illustrate to After-Effects if everything is on the same layer? My UI guy put everything on the same layer but I can't transfer anything to After-Effects.
You may want to save each artboard to a separate file (which you can do in the save options).
And for each file create separate main layers for elements you want to animate.
AE does not support multiple artboards and will only load the first one. You need to export them separately and import the resulting individual AI files.