Threejs saving object to json with animations - animation

Question

I can successfully load a 3D object from, for example, an FBX File, load and play it's animations. The problem is that, after doing what i gotta do with it, i need to save the changes. To do that, I'm saving the object and the object animation clip to a JSON. I can, now, load the 3D Object in the scene, but no animations will play(it'll stand on T pose), but trying to load the saved clip on the object loaded from FBX will play the animation without a problem.
After reading the resulting JSON from the 3D Object, a lot of data seems to be missing, that's why trying to play animations does nothing.
How can i save the loaded FBX model to a .json and keep the important data? I remember seeing some post about putting some flags on the toJSON method, but couldn't find anything similar again.
Edit:
Using GLTF seems to solve this problem, but three.js GLTFLoader isn't loading any kind of .gltf object and i don't know why, for all of the objects i've tried using (used objects from threejs.org GLTFExporter examples) i'm getting the same error:
TypeError: Cannot read property 'geometry' of undefined
at GLTFLoader.js:2572
That's how i'm trying to load it:
loader_helper.gltf_loader.load("./src/data/scene.gltf", function ( gltf ) {
console.log(gltf); // This is enough to get the error, altough i've tried
// mimicking the FBX import, but getting the same errors
});
Edit: Using https://gltf-viewer.donmccurdy.com/ to view the object, the object i exported was completely bugged ( https://imgur.com/a/yLimuWp ) and i didn't notice, but i tested the bugged object three times, so i thought the problem was in the loader, it is seems to be loading fine using a non-bugged object. Although the export is bugged, the object skinned mesh is loading without issues and only the mesh is being loaded with, wel.. you saw it. https://imgur.com/a/evGmnOG
That's how i'm exporting the scene:
// this is a button.onclick function
var exporter = new THREE.GLTFExporter();
exporter.parse( that.scene, function(gltf){
var stringfied = JSON.stringify(gltf, null, 3);
require("fs").writeFile( "./src/data/scene.gltf", stringfied, 'utf8', function(err) {
console.log(err); // saving it to file with nodejs file system
});
console.log(gltf);
} );