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I'd like to know the answer too. It seems the Animation Editor in the External Editor doesn't save new animations.
You may just need to create the animations in the Database (F9) first, then touch them up in the Animation Editor (e.g. to move battlers around). If this is so, then please let me know so I can write it in the wiki.
Preferably there will be a script solution which makes the Animation Editor save new animations. If anyone can figure it out, again, let me know.