Assetbundle from different project. Resetting script references?

So here is a crazy situation I need help understanding. I have two projects. Duplicated from one to another. (By simple files/folder copy). On one I removed all the data/context. I kept all the scripts. The other has both. On the one with the data I created bundles (using addressable) and loaded them up to the cloud. On the second one I added code to download the bundle and open up the scene contained with it. Everything works great. I was a little surprised by that

Then I had a need to move some of the content to the project that did not have any content, locally. So I exported the scene and its dependencies (but no scripts) using Assets->Export and then imported the scene to the second project using Assets->Import Custom Package. And almost all of my script references are gone!!. Why not ALL no idea.

Any thoughts on what might be going on here? Anyways for me to re-reference the scripts. Maybe with some code?