Reproduction steps:

1. Open "MinimalRepro.zip" project
2. Click on "NewAssembly Main" in the Project window
3. In the Inspector window add two objects in the "References"
4. Drag "DummyAsmDef1" to both of the fields
5. "Apply"
6. Re-open the project
7. Click on "NewAssembly Main" in the Project window
8. Both "References" are missing and there are two "AssemblyDefinitionException" errors

Expected Result: The AssemblyDefinition references should stay the same after re-opening the project
Actual Result: the duplicate AssemblyDefinition references are missing and two "AssemblyDefinitionException" errors appear

Fixed in: 2018.2.0a5, 2018.1.3f1

Reproduced with: 2018.2.0a1, 2018.1.0b6, 2017.3.1f1, 2017.3.0b1
Did not reproduce on: 2017.3.0a7 (Assembly Definitions implemented only from 2017.3.0b1)