I looked into the issue, and I think it has something either to do with Godot C# loosing data when building OR because the data is not marshalable (serializable) it gets lost on rebuilds. There was a few issues about it on GitHub, but nothing definitive. I will do more looking into it soon to see if I can find a viable solution, but short term you may want to close and then reopen the scene file after building, as it looks like it may be a Godot bug.