Steps to reproduce:

1. Create a object with a built-in material
2. Create a prefab, save the scene
3. Have that scene, with a prefab instance, and the prefab in the project browser
4. Go to RP converter -> Built-in to URP, select Material Converter
5. Perform the conversion, see that the material is changed, on both scene and prefab, but, the scene prefab instance, now is an override.

Actual results:  Material is changed with a prefab instance override

Expected results:  Material is changed only in the prefab, If a prefab instance already had a material override the material is changed in the prefab instance, and in the prefab.