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Fixed in 2019.3.X, 2020.1.X
[Asset Database V2] GameObjects and Prefabs lose references to Assets when Assets are moved to a different folder
How to reproduce:
1. Open the user's project
2. Create a new script in Project Browser
3. Create a new GameObject
4. Attach the created script to the GameObject
5. Move the created script to the 'Script' folder
Expected result: GameObject does not lose the reference to the script
Actual result: GameObject loses reference to the script
Reproducible with: 2019.3.0a1, 2019.3.6f1, 2020.1.0b2, 2020.2.0a3
Not reproducible with: 2017.4.38f1, 2018.4.19f1, 2019.2.21f1
Note: Bug introduced with Asset Database V2 which was introduced in 2019.3, the bug is not reproducible when switching Asset Database to V1. The bug only appears with GameDevHQ filebase installed, deleting it (found in Assets -> Asset Packs folder) fixes the bug.
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Resolution Note (2020.2.X):
Basically what happens is, in v2 the user is responsible for moving the .meta file of an asset(warning is logged), and in v1 we patch up metadata and move the file in the following refresh. The complexity of this patching process meant that we decided not to do the same for v2.