Steps to reproduce:

1. Add sphere to scene.
2. Add cube to scene.
3. Make cube child of sphere.
4. Drag sphere to project browser.
5. Delete cube from hierarchy.

This used to give a warning that you are breaking the prefab connection and asked you whether you want to proceed. Now it will simply delete the child -- apparently without breaking the prefab connection which is cool as it allows you to edit the prefab that way -- but in the scene view the prefab instance will no longer be marked blue but rather be white like a non-prefab object.