I ran into the same problem when upgrading an existing project from Unity 2018.2.20f1 to Unity 2018.3.14f1. Unity’s upgrade process breaks all of the prefabs in the scene and fills them with missing references.
Fortunately, I have excellent backups, so I was able to revert back to my project in 2018.2. However, I cannot do that forever, since there are some bugfixes that are only available in 2018.3 and 2019.1. Unity has stopped supporting 2018.2, so certain bugs in that branch will not get fixes. To get those bugfixes, I have to move to 2018.3 or 2019.1. For example, there are some VR bugs that fall into this category.
I am really surprised by these prefab issues. I understand that 2018.3 changed the prefab workflow. I get that. However, I expect Unity’s upgrader to be able to convert a working 2018.2 project to 2018.3 without breaking every prefab in the scene. I waited a while to give Unity a chance to shake some bugs out. At this point, I tried using 2018.3.14. Unity had alphas, betas, and now 14 additional releases. That should have been plenty of time to get the new prefabs working right and get the project upgrader code working right.
I am expecting too much? I am doing something wrong? Or is Unity 2018.3 really this buggy?
UPDATE: I did manage to figure out why there were missing prefab references in my project after upgrading. It was caused by compiler problems related to package manager. Here is a link to my thread about that.