Scaling bones in blender still introduces wierd rotations on the parent bone.
So avoid scaling bones in animations.
Re blender NLA tracks.
I much prefer working without and having a single file for each animation to edit.
The idea behind the system is the opposite. Having one file where you can access and export any stored animation. Oneslty, its confusing on the best of days. When you are 5 hours deep on animating it only gets worse, so i avoid it alltogether.
Generally speaking people are oftent told:
Do not animate IK bones.
This is BS. They are supposed to directly follow their parent bone, so they can be peogrammatically moved/adjusted as the code calls for.
However, its looking like your NLA track has some issues with IKstuff that has been removed or similar.
Best suggestion is to create a new file and copy the armature over - you’d think.
But the paste process can actually bring in the nla tracks, so you have to be aware of it / delete them manually after pasting.
For simplyfying exports you can probably use my plugin.
Default functionality is to use a mannequin rig, but if you name the armature Root you can export any armature with the correct pre-set settings without having to remeber what is what…