1. Create a new scene.
2. Add it to build settings.
3. Create a new folder in Project. Move created scene to folder.
Note: Open Build Settings and check that scenes are available.
4. Save and reopen project.
5. Open build settings.

Actual result: Scene is grayed out, you need to add scene again or move it back to place.
Expected result: Scenes in their new location are available.

Works fine in 5.4.0b1. Reproduces since 5.4.0b2.