I’ve had some success with exporting to FBX, reimporting into a fresh Blender file, then re-exporting it to FBX from the new file. This has worked for some animations and missing material slots as long as the thing works in the new Blender file. I still don’t know why it happens, so I don’t have a “true solution” to this yet, but I’ve used this as a workaround for some of the issues I’ve run into. Hopefully this will help you out some too.
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