Files differs in more aspects, but one that cause saving the keyframes is your "CRUMPLE" action saved in your "broken" file.
There is several ways to fix it:
- Delete this Action in your original file before Linking or
- Manually set Make Library Override by right click on item in Outliner of the file or
- Go to Dope Sheet editor switch to Action editor and click on chain icon to make it local or click on X icon to delete Action
Note: When you use "Link" operator (to bring some elements from another blend file) you can't modify them. For that blender use Library Override to make it happen. Any linked element in Outliner that is linked from external directory is using "chain" icon to indicate that. To be able to manipulate with linked object you have to Add Library Override, that creates something like information layer that stores changes from original.
I have never used Library Override before so I'm not experienced here ... but for some reason Actions and Materials are kept Linked for Make Library Override Hierarchy command by default. If it is a bug or expected behaviour ... I don't know (probably in common use you don't want to modify those). Anyway as I wrote you have to delete or Override specific items manually.