Make sure you have a backup. I mean seriously what did you guys do to the engine? LOL. 
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Hi
please try to reimport all your fbx files.
Due to an issue with the model importer models are not correctly imported when upgrading from 18.2 to 18.3.
The issues is fixed in beta 3
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Thanks for the reply, great to know post trying this. I couldn’t even load the build I had to remove UnityConnectSettings to keep the upgrade from crashing. Also it took 28 hours to upgrade and hash from 2012.2.7
I am posting this in case someone was silly enough to not backup their projects. This is a Beta people so expect things to happen!
But my small/basic project from 2017.2.7, when imported in 2018.3, was erased.
When imported in 2018.3, there was only Asset folder with sample scene.
I won’t be testing the 2013.3 betas if this won’t be fixed.
Importing prefabs and working with them is pain and unintuitive in 2018.3.
reimporting did not fix in my case, I did even delete the whole Library folder.
I’ve a bug reported for this issue, but they where not able to reproduce, I’m trying to strip my project to send them. New prefab system has kicked me out of beta system pretty much :\
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Me too. Did you use Blender for importing prefabs ? Maybe Blender exporter is not compatible with new prefab workflow.
But, my whole scripts and folders were deleted too so I don’t know what is happening,.
I export from 3dmax to fbx, 2014 version I believe.
I did not get files deleted but my prefabs where reseted when instanced or draged into scene. What is crazy tho is that I did add a unitypackage with one of the reseting prefabs and they where unable to reproduze :\
So it looks like they need whole project or at least a working project as it may be a config thing. I’ve a shitty DSL and a monster sized project…
I also got this issue. I’ve exported 100s of .obj files from MagicaVoxel, and any prefab that was a direct reference to any model got missing on every scene. Now, most non-prefabs got fatal scale and position changes, which is something that I don’t get. I’ve filed a bug report too, but they haven’t answered it yet.
I really hope this gets fixed on the next update, because it’ll be a pain to remake all of the levels in my game.
Case number: 1082061
Aparently they whant to wait till 2018.3 I cant happen to understand how having such a criticalnissuenthey dont plan having this fixed by 2018.2.
Apparently, this issue is super easy to solve. In my case, at least. Just Right-Click the Project tab (not the tab, but inside the window) and press Reimport All. Depending on the size of the project this can take up to hours. Mine is a few gigs and got through really fast.
What it does is essentially rebuild and/or reimport all - every single one - of the assets in your project, leading to loading the correct values. Now, why is this needed? I don’t really know, but that’s how you fix it.
The problem seems to be related to Unity’s importer exclusively, not to any modeling software (or any at all).
I’ve been using 2018.3 without any problems since then. Really, it’s amazing and worth it. Prior to this, I had all of my levels messed up. Then they got fixed.
So, the answer for those who are scared off of 2018.3 - just joking, guys - is: don’t be afraid. It is not scary. Just a button pressed and bam, everything gets fixed.
Disclaimer - This is based on what happened to me, so please be kind. 
To fixe the prefab itself it was reported at least on b1 that reimport all would not work (they where looking at it why not) . so simply list all your project prefabs select all and hit reimport, may be this is fixed in b2,
This still applies to b3.
Yes the fix is waiting in the release queue…
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Well, I did it in b2. I have no idea if it still applies or not to b3 or b4. For me, it works.