I'm still getting used to the Animate workflow... If I create a small scene in one file with movie clip symbols, can I copy this entire sequence into another file as a movie clip? How many movie clips can be nested within each other? Also, can scenes be strung together without ending up with a thousand layers?
Yes, you can copy a movie clip symbol into another movie clip symbol. I don't believe there's a limit on how many movie clips you can have within a movie clip. In answer to your stringing together scenes question, I would export each scene as a .mov file and then bring them into Premiere and edit them all together that way.