Steps to reproduce:

1. Open attached project
2. Open scene "repro"
3. Run it. Two child objects will be instantiated for cubes
4. In scene view, using Area selection tool, select Cubes (spheres will be selected as well)
5. Notice that transform handles are visible - this is expected
6. Exit play mode
7. In scene view, notice that there are no transform handles anymore

Note: this issue happens because the first object which is selected is instantiated sphere. Once exiting play mode that sphere is destroyed, and together with it - transform handles are destroyed as well

Reproduced with: 5.2.4f1, 5.3.4p5, 5.4.0b17