ARCarr - Thanks for the detailed information! This will be quite helpful for trying to figure out what is going on. I'm wondering if it's a Window specific issue, though I'm still not sure why it is occurring, as I haven't been able to reproduce it on my machine. I will need to test again though, maybe something in a recent Godot version changed something.
For issue 6393: have you tried closing and reopening the Godot editor? If you have multiple instances of the Godot editor open, closing all of them and then reopening the scene may help. I believe it is related to trying to save the ".tscn" file.