The new add-in doesn't have the 'convert to plain text' functionality just yet unfortunately. There is a workaround you can use, but please note that this method will remove every hyperlink in your document, not just the Sciwheel ones. If you have other hyperlinks you want to keep you could either select sections of text instead of selecting everything, or just add the desired hyperlinks again if that's easier. Here's the method:
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Create a copy of your document. This is important so you still have a linked version of the document you can go back to. Once the hyperlinks are removed the add-in won't be able to format the citations and bibliography.
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Select the text you want to remove the hyperlinks from. To select all text in your document, press Ctrl+A on Windows, or Command + A on Mac.
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Press Ctrl+Shift+F9 on Windows or Command + 6 on Mac to remove all hyperlinks in the selected text.