Just posting this bug report in case other people look for it! It's a [known issue |https://ludiq.io/bolt/known-issues#prefab-reimport]with a simple fix:

When instantiating a prefab in Unity 2018.3, you might run into an issue where all its Bolt components are reset to their default state.

That means, for example:
* The source of machines is reset to Macro, and the macro reference is None
* The variables component is entirely blank
* A reference to this prefab elsewhere shows a null or missing

This happens for prefabs in projects that were created in the *old prefab workflow* (Unity 2018.2 and below) then opened in a newer version of Unity with the new prefab workflow (Unity 2018.3 and above).

The solution is simply to *Reimport* the affected prefabs. You can do so by selecting the prefabs, then choosing Assets > Reimport.

If you want to make sure you did not miss anything in your project, you can also use Assets > Reimport All. Note that a full reimport can be very long depending on the size of your project.
 
Bolt Version:
 
Unity Version:
2018.3
Platform(s):
 
Scripting Backend:
 
.NET Version (API Compatibility Level):