Steps to reproduce:

1. Open attached project "774962.zip"
2. Open scene "A"
3. In hierarchy, select Terrain
4. Open Terrain Settings tab
5. Uncheck Draw field found under "Tree & Detail Objects"
6. Save scene (CTRL + S)
7. Open scene "B"
8. Open scene "A"
9. Notice that change isn't saved

Workaround: before saving, move some object found in scene to make scene dirty OR use Save scene as... and save on itself

Not reproducible: 5.2.4f1
Regression introduced in: 5.3.0a3
Reproduced with: 5.3.3p1, 5.4.0b8