Are you able to post an example FLA somewhere?
On C# and Unity, it's amazing. You don't have to use one tool for every.
I will upload the fla and swf files on a google drive and send you the link tonight. Really want to get this figured out.
Here are link to the files via google drive:
I made the Tears animation and then used that in the Crying Maidana Head - I feel the way I approached this part could have something to do with it.
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With spritesheets you only get what you can see when scrubbing the timeline. If a movieclip is one frame long you only get that one frame, even if it contains other things that have more than one frame. If you made the tears movieclip be 20 frames long, you would still just get the stationary tears, because those are movieclips.
If you want a spritesheet which is the head squinting, and one run through of the tears falling, you could duplicate the head animations on the timeline, to say 25 frames. Then select the tears movieclip and change it to be a Graphic instead. Inside tears you would select the individual tears and make them be graphics too, and make the tears timeline be 25 frames long. Set each tear graphic to Play Once, in the Properties panel, and also set tears to play once.
With all that done you should be able to scrub the outermost timeline, and see the tears falling. If you get that far you can then convert it to a spritesheet, which should have the head and the tears animating.