Also to add to this.
When you edit an external JS link file. You will be prompted to either update the project version or not.
This is a good feature but it would also help with the above and current design, for the the Linked JS files to have a Button to convert to a Hype Function.
This would mean the source can still be edited either with the inbuilt editor or external editor.
But you now have a separate hype function to work on and use.
Or another approach and maybe more manageable is to have a preference to convert imported JS files to Hype functions automatically and leaving you with a new Hype Function and the original as is and not linked or showing in the resources.