Reproduction steps:
1. Open the attached project “ReproProj“ (3D URP project created with 2023.2.16f1). Alternatively, it is possible to create a project with 2023.2.0a17 or higher and open it in affected Editor version.
2. Try to create a new scene (File > New Scene) and observe the Scene Templates
3. Observe “Packages/com.unity.render-pipelines.universal“ folder

Expected result: There are scene 4 templates when creating a new scene and URP package folder is not empty
Actual result: Package references disappear, URP scene templates are not available and URP package folder is empty in the Project window

Reproducible with: 2023.3.0a14, 6000.0.0b13
Not reproducible with: 2021.3.36f1, 2022.3.21f1, 2023.3.0a13

Reproducible on: Windows 10, Windows 11 (by user)
Not reproducible on: No other environment tested

Notes:
Also affects most other packages
This can be fixed by deleting and reimporting the missing package or reimporting the project (Assets > Reimport All)
Can cause a crash when deleting URP if the project has dependencies to it (not reproduced by CQA)