Reproduction steps:

1. Open "MinimalRepro.zip" project
2. Open "Git Bash" and "cd" to the project directory
3. In Git write "git status"
4. Notice that there aren't any data changes to the "New Terrain" object
5. In Git write "git add ." -> "git commit -m "Commit 2""
6. Rename the Objects in "_TerrainAutoUpgrade" to something simple (e.g. "layer1", "layer2")
7. In Git write "git status"
8. Notice that there aren't any data changes to the "New Terrain" object

Expected Result: After upgrading Terrain or changing Layer data, the Terrain objects data should explicitly reference the upgraded/changed Layers
Actual Result: Terrain Layers are not explicitly linked to the Terrain object after upgrade

Fixed in: 2018.3.0b8

Reproduced with: 2019.1.0a4, 2018.3.0b5, 2018.3.0a4
Did not reproduce on: 2018.3.0a3, 2018.2.12f1, 2018.1.9f2, 2017.4.13f1 (Terrain upgrade was only introduced in 2018.3.0a4)

Note:
Need to have Git Bash installed and set-up

After renaming the Layers and restarting the Editor, the original Layers are re-created and the renamed ones get unlinked from the Terrain Object