so about the prefabs that disappear

it also happened in 2018 LTS, isn't that when you guys switched over to Neo prefabs?
so it seems to happen with 100% consistency when you import a project from a previous version of unity and some of the API was removed, like, say, [RPC]

Definitely not user friendly
A good motivator to fix scripts though.

since it's a deeply rooted bug I logged it in 2018LTS, you can trace the root more easily like that
case #1240728


Once the scripts are fixed unity does another pass at converting assets.

That's odd so I looked through the project and found this AssetPostProcessor. Could this be the reason for such behavior?

using UnityEngine;
using UnityEditor;
using System.Collections;
using System.Collections.Generic;

public class GeneralPostProcessor : AssetPostprocessor {

    void OnPreprocessModel ()
        ModelImporter importer = assetImporter as ModelImporter;
        importer.materialName = ModelImporterMaterialName.BasedOnMaterialName;
        importer.materialSearch = ModelImporterMaterialSearch.Everywhere;