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It seems to be that reimporting the libraries is somehow breaking the prefabs.

Then copying over everything including libraries. I was able to fix this by updating the original Unity Client I was copying from, to the latest version, and the Unity version on the target computer to the latest version. If I can't get this to work I will have to just keep working on the old computer since I am not able to transfer my project successfully. I will try having both set ups have the same version of unity before moving things over to see if that makes a difference. Keeping the meta files did not solve the problem for me. Many prefabs also can't be dragged into the scene or a new scene. When I open the scenes my prefabs are missing inside the scene. The library is reimported (or seems to do some loading). The unity versions are different and I am prompted to upgrade everything to the latest version after transfer.

When this didn't work because of the missing prefabs I tried just copying over the entire unity folder via USB. I first tried to copy over the project by git. I am having the same problem when importing to a new windows machine (windows 10).