One way to get around this is to:
First in case you want to keep the double hyphens as they are:
- Use the search/replace to replace the double hyphens to some unique text e.g _double hyphen_
- Run smarten punctuation.
- Replace the unique text back to double hyphen.
Or if you want to convert them to anything else
- Use the search/replace to replace the double hyphens to whatever you want.
- Run smarten punctuation.
You can automate the process using the
Editor Chains plugin, which allows you to invoke the whole sequence from a menu entry or a keyboard shortcut.