Allow users to 'Save as...' similarly to any other application we use. Currently we can only copy a project. But changes to your project must be saved before copying! So if you open a project, make a few changes, then want to preserve the original project and save this modified version with another name, you simply can't. You must save the changes, then create a copy with another name, which will be the project at that point in time. So then you have two projects which are exactly the same, with different names.
Someone can argue that you should make a copy prior to modifying your project. But that's not how every other software work, and we have a mental model of 'Save as...' as something that allows us to change a file and save it with another name preserving the original version.
That's particularly useful for doing thematic analysis, when we merge nodes, move them about and try to simplify the hierarchies, but you want to keep a track of the evolution, say one file per day, to be able to go back to a specific version and redo analysis, for example.