Prototype interactions disappear after a library update

I have 3 libraries. One is a component library, second is more complex components, and the third is page templates. I have separate design files that I import any changes from the libraries. The design files are where the prototype interactions live. The problem i have is that some of the interactions on specific components will consistently disappear every time i update the design file from any of the three libraries. Some component interactions will only sometimes disappear after an update. And some will always remain. Why is that?