Reproduction steps:
1. Open attached project "1216508_resolution"
2. Go to Edit > Project Settings > Player > Resolution and Presentation
3. Set Fullscreen Mode to Windowed, Default Screen Width and Height to 640X480
4. Got to File > Build And Run
5. In the Player settings, change Fullscreen Mode to Fullscreen Window (Default Is Native Resolution becomes checked automatically)
6. Got to File > Build And Run

Expected result: Build is run in default native resolution
Actual result: Build is run in previously chosen resolution (640X480)

Reproducible with: 2017.4.36f1, 2018.4.17f1, 2019.2.21f1, 2019.3.1f1, 2020.1.0a22

Workarounds:
Building in Fullscreen Window Mode with Default Is Native Resolution unchecked and then building again with it checked
Setting Default Screen Width and Height to the wanted resolution

Note:
Following these steps in 2017.4 build is not in Windowed Mode when Default Is Full Screen option is disabled but the issue still persists