How to reproduce:
1. Open the attached "HideFlagBug2.zip" Project
2. Open the "HideFlagTestPrefabMadeWith2018.2(original).prefab" in Prefab Mode
3. Change any Value on the Transform of the root GameObject
4. Save Prefab
5. Close and Open Prefab again in the Prefab Mode

Expected Behavior: The "HideFlags.DontSaveInEditor" is respected and only one "Should not be saved" Child is present
Actual Behavior: The "HideFlags.DontSaveInEditor" is not respected and "Should not be saved" Child is duplicated

Reproducible with: 2018.4.1f1, 2019.1.4f1, 2019.2.0b3, 2019.3.0a3

Note: Once the Prefab is saved in the 2018.3.0a6 or newer version - its serialization is changed and the issue does not reproduce anymore. If you open the Prefab in the text editor and search for "Should not be saved" you can see that it was serialized, even though it should not be. All the affected prefabs must be saved in 2018.3.0a5 or lower versions.