Adding the references using the editor, it would not be able to find them and throw the exception

To reproduce:

1. Download attached project "Digimon 3D.zip" and open in Unity
2. Open "Application" scene
3. Open "Digimon 3D" folder and select "Digimon 3D.asmdef" file
4. In Inspector window fill Missing Reference fields with these files:

TheDialgaTeam.Modules.System.asmdef
TheDialgaTeam.Modules.UnityEngine.asmdef
TheDialgaTeam.MVCC.asmdef

5. Click "Apply" button

Expected Result: Files will be applied in References fields
Actual Result: All those selected files will disappear from References fields and Console will be spammed with the exceptions:

AssemblyDefinitionException: Could not find assembly reference 'TheDialgaTeam.Modules.System'
AssemblyDefinitionException: Could not find assembly reference 'TheDialgaTeam.Modules.UnityEngine'
AssemblyDefinitionException: Could not find assembly reference 'TheDialgaTeam.MVCC'

Notes:
- This issue appears on Windows and OSX
- It works fine in Visual Studio

Reproduced on Unity 2017.3.0b1, 2017.3.0b2 and 2017.3.0b3
Could not check for regression on 2017.2, because files becomes corrupted