Repro steps:
1. Open the attached project "import-overwrite.zip"
2. Note that the scene "SampleScene2.unity" is empty and open scene "SampleScene.unity"
3. In the Editor, go to Assets > Import Package > Custom Package
4. Import the attached package "SampleScene2.unitypackage"

Expected results: importing "SampleScene2.unitypackage" either creates a new scene with three cubes in it, or it is possible to choose "SampleScene2.unity" in the Import Unity Package window so that an empty scene would be overwritten instead of a filled one
Actual results: it is impossible to choose "SampleScene2.unity" in the Import Unity Package window, the imported package irreversibly overwrites "SampleScene.unity" and instead of three spheres, three cubes are now seen

Reproducible with: 2018.4.0f1, 2018.4.23f1, 2019.3.0a1, 2019.3.14f1, 2020.1.0a1, 2020.1.0b9, 2020.2.0a1, 2020.2.0a11

Notes:
- Importing "SampleScene.unitypackage" changes "SampleScene.unity" back to a scene containing three spheres so that the issue would stay visible