Thanks, that's very helpful. I managed to track down the issue, there was a problem with duplicate ID assignment with prefabs, which confused the system.
I uploaded a version of the binaries with the fix: http://bearishsun.thalassa.feralhosting ... v0.4p0.zip
Note that this won't fix your existing prefabs, but it should prevent the issue in the future. Make sure to delete all existing .prefab files as they're corrupt.
Also note I cannot guarantee that this was the issue that caused your problem because I don't have the exact set of steps you used when you created the scene, but I extensively analyzed your scene and it most likely was the culprit. However it's always nice to confirm, so if you decide to create a similar scene again let me know if it works.