How to reproduce:
1. Make sure that you have Android or iOS module downloaded
2. Create a new project
3. Open preferences and leave the window
4. Build and run the project (it can be standalone, andoird,.. build)
5. After it is done, check External Tools in preferences
6. Notice that Android setting are gone
Note: Closing and opening preferences window solves the issue

Reproducible: 5.6.0a3, 5.6.0a5
Not reproducible: 5.5.0f3, 5.6.0a1

Issue is no longer reproducible: 5.6.0b11