How to reproduce:
1. Open the attached "case_1149316.zip" Unity project
2. Open the "Parent" Prefab Variant in Prefab Mode
3. Swap the order of the GameObject and the Prefab in the "Parent" Prefab Variant
4. Save the "Parent" Prefab Variant and re-open it in Prefab Mode

Expected result: "Child" Prefab and "Child" GameObject remain in the "Parent" Prefab hierarchy
Actual result: "Child" GameObject disappears and its Components merge with the "Child" Prefab Components

Reproducible with: 2018.3.14f1, 2019.1.0f2, 2019.2.0a13, 2019.2.0a2
Not reproducible with: 2018.3.11f1, 2018.4.0f1, 2019.3.0a3, 2019.1.0b9, 2019.1.0f1, 2019.2.0a9

Notes:
1. The issue is reproducible when the child GameObject is above the child Prefab inside a Prefab Variant, the child Prefab has an unapplied Component, and both the child GameObject and the child Prefab have identical names. Not reproducible on 2018.4.0f1 and 2019.1.0f1 versions.
2. The issue has been fixed in 2019.3.0a3