Hi there! With decks as large as Anking you probably will need to run sync quite a few times before all the media will be in sync, it can take a few but it gets closer each time since it picks up syncing media files from where it left off.
https://github.com/ankidroid/Anki-Android/wiki/FAQ#why-doesnt-my-sound-or-image-work-on-ankidroid
-Mike
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