Well, actually your file is working. Nothing is broken.
I tried to see what is the result of the exported .glb file inside the three js viewer at this url: https://gltf-viewer.donmccurdy.com/
What is different is that the shapekeys are not visible as an animation but as a morph target.
Try putting your mesh inside this viewer, and you'll be able to see this :
On the right side of your screen, there is a lot of dropdown menus. Open the Animation and Morph Targets ones.
Your shapekeys animation can be found under the Morph targets -> "Left Eye Large v2" and "Right Eye Large v2".
On the screenshot, I put them at a value of 1. This value can be changed in the range [0 - 1] and for each of the concerned meshes.
So I think you should try to use different approach inside your three js code to be able to play it as an animation.
Check out the example of three JS regarding morph targets
Hope this will help ! :)