I created 40 feathers using ALT+D. After saving, they all collapsed into one pen of the same size. Why and how do I fix this?
You have enabled auto keyframing, which has added a keyframe to the first object:
Yellow diamond icon represents the keyframe.
After opening file or changing current frame, objects moves to it's keyframed position, which is the same for all objects. Open dope sheet editor and remove keyframes.