Steps to reproduce:
1. Open QA attached project
2. Select "NewShaderVariants" file in Project view
3. Set "AssetBundle" to shaders or tescene or anything you create
4. Open Project settings -> Graphics and at the bottom of the window press "Save to assets..."
5. Overwrite "NewShaderVariants" file when saving
6. Select new "NewShaderVariants" file and observe the "AssetBundle" being set to "None"

Expected Result: When overwriting the ShaderVariant collection the AssetBundle reference would be preserved
Actual Result: The AssetBundle reference is destroyed, leaving "None" in its stead

Reproduced on 5.4.5p1, 5.5.3p1, 5.6.0f3, 5.6.0p4, 2017.1.0b4, 2018.4.27f1, 2019.2.21f1
Not reproducible: 2019.3.0a1, 2019.4.12f1, 2020.1.9f1, 2020.2.0b6