The issue might be a merge conflict caused by working on the project simultaneously on different machines. This happened to me by having the project open on laptop and desktop at the same time. Digging around, I found this reddit post, with instructions on how to change the .tscn-file with a text editor. The trick is correcting duplicate id's of loading resources caused by the merge conflict.

https://www.reddit.com/r/godot/comments/6ntejk/tips_how_to_fix_merge_conflict_with_tscn_files/