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You can't modify files outside of Sigil and have changes to those external files reflected in Sigil. Sigil maintains its own copies of files once imported. There is no connection between them and the original files anymore. Nor will there ever be.
If you need to modify html files (that are already IN Sigil) with an external editor, then use the Open With feature. If you right click on an (x)html file within Sigil's Book Browser, you can select "Open with", and then choose the executable of the external editor you'd like to use.
But for the automated process you desire, I doubt that will be sufficient. What you are describing sounds like the perfect candidate for an Import plugin.
I'm afraid there's never going to be an integral Sigil feature that synchronizes its internal, epub file structure with a corresponding external file structure. It's just not feasible.
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