Referencing will not work with any export to augmented reality formats, so make sure your model, rig, animation, and any other elements in your scene are all in the same file.

Should you already have done your animation on a referenced rig, Maya has an easy way to transfer your animation keyframes back to the base file: Maya official ATOM help page

Make sure to replace the namespace with a blank to ensure the animation imports back to your rig, like so: