I am working on a 300 or so page document that has in it references to other articles that appear on the internet here and there. In some of those references, InDesign made hyperlinks out of the few words that are the reference and placed a box around those words. I don't want these references to be links and I don't want the boxes. How can I get rid of the links and the boxes in one step and not one at a time (there are lots of them)?
Well, InDesign doesn't do this (unless asked to), so the hyperlinks were there in the original document that you imported.
Call up the Hyperlinks palette, click the first one to select, scroll down and shift+click the last to select them all, then click on the lil' Trash Can or select "Delete Hyperlink/Cross Reference" from the palette menu. ID will ask if you want to 'convert to text' but that's only applicable for cross references.
What are cross references?