Load the file in ScripturePad like normal
Do a Ctrl+A to select all the text. (It should all be highlighted)
Then do a Ctrl+C to copy all the selected text.
Click the New Button in the ScripturePad Toolbar to make a blank document. (The original one will disappear.)
Then click the mouse in the blank page and hit Ctrl+V to paste in the copied text.
Then try to link the refs.