To reproduce:
1. Create a new project
2. Set the target platform to Store Apps and sdk to Phone 8.1
3. Import the attached image and use it in the player settings (Under Application Icon, Scale 240%, 106x106)
4. Build
5. Open the generated solution, inspect the icon
6. In unity player settings, remove the icon
7. Rebuild on the same folder
8. Inspect the icons - the icon you removed in Unity also got removed in the solution

This is the only icon that acts this way, other icons to not get overwritten.