How to reproduce:
1. Create a new project
2. Add a c# script
3. Set Scripting Runtime Version to legacy (3.5)
4. Close editor
5. Copy ProjectSettings.asset and store it outside the project
7. Set Scripting Runtime Version to stable (4.x)
8. Close editor
9. Replace ProjectSettings/ProjectSettings.asset with the previous version of the file stored in step 5.

Actual result: Scripting Runtime Version didn't change from outside when you switch scripting runtimes from 3.5 to 4.x and vice versa we can't really change Scripting Runtime Version by just reading the ProjectSettings/ProjectSettings.asset file (e.g. using source control software), it always must be changed manually in PlayerSettings inside Unity Editor

Reproduced with: 2018.1.0b10
Not reproduced with: 2017.3.1p4, 2018.1.0b8, 2018.2.0a4
Regression since: 2018.1.0b9

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Fixed on:
2018.1.0b12, 2018.2.0a5