How to reproduce:
1. Open the "BuildFailure" project
2. Open the "main" scene
3. Press Play (notice the script "hello" is working)
4 Try to build the project
5 Press Play again, the script reference is missing

Expected Result: The build failure doesn't affect the Editor.
Actual Result: The script references in the scene are lost.

Reproducible with: 2017.1.0p3, 5.6.3f1, 5.5.4p2.
Not reproducible with: 2017.3.0a3, 2017.2.0b6.

Note: with 5.6.3f1 and 5.5.4p2 the script references are not lost, but Unity won't let you enter play mode because of "compiler error".