Steps to reproduce:

Create a new URP 3D Project
Make sure the "Use new Hierarchy window" is enabled in Preferences > Editor
In the Hierarchy, create a Cube GameObject
Drag it to the Project window to create a prefab
In the Hierarchy, click on the search icon to add query blocks
Select Component > Any
Observe only the prefab is visible in the Hierarchy
Click on the ">" next to prefab to open it in context
Click the "<" to exit prefab context
Observe the Hierarchy

Actual results: The query block remains visible in the Hierarchy search field, but the Hierarchy is no longer filtered and non-prefab GameObjects are shown

Expected results: The Hierarchy should remain filtered according to the visible query block after returning from Prefab Mode in Context, or the query block should be cleared if the filter is no longer applied

Reproducible with versions: 6000.3.15f1, 6000.4.7f1, 6000.5.0b8, 6000.6.0a5

Can’t test with versions: 6000.0.75f1 (New Hierarchy not available)

Tested on (OS): Ubuntu 24.04, macOS 26.4

Notes:

Closing and reopening the Hierarchy window clears the stale query state
Reopening the scene does not clear the issue
Resetting the Editor layout also removes the query block