How to reproduce:
1. Create a new template URP/HDRP project
2. Duplicate the 'SampleScene' Scene and open the duplicated Scene
3. Delete 4-5 GameObject from the Hierarchy
4. Save the Scene and close the Editor
5. Delete Library folder
6. Reopen the project
7. Build for Standalone
8. Once the player is built save a copy of the build folder
9. Delete Library folder
10. Open Editor
11. Perform another build
12. Compare the results of the first and second build folders (for macOS FileMerge can be used in order to compare the results or in terminal: diff -r -q /Folder1 /Folder2)

Expected result: The same set of inputs produce files that are identical
Actual result: The Level files change

Reproducible with: 2019.4.14f1, 2020.1.12f1, 2020.2.0b7, 2021.1.0a3

Notes:
- Reproducible on Windows and macOS
- Screenshot of the issue is attached in Edit