Armatures and Shape Keys

I can’t seem to figure this out, and the threads I searched on here are slightly off or confusing to me.

What I am trying to do is export an animation made using an skeleton to a format that doesn’t support bones, but it does use Shape Keys.

But the bones don’t deform the actual mesh, so when you enter edit mode to apply a shape key, it reverts back to the object’s initial shape. I am guessing this might be something simple I don’t know about or something that blender just can’t do easily. I am a noob when it comes to armatures so I don’t really have a clue.