I'm writing this in case someone else has the same problem. What I ended up doing was pretty simple, not sure why it didn't occur to me earlier.
I signed out of Opera to stop the sync, then closed it and switched the bookmarks file with the old one. Restarted Opera, verified that all of the bookmarks were recovered, and then exported them to an html file. I signed back into Opera and the bookmarks immediately disappeared after it syncronised. But now I could import the html file with the bookmarks that I needed. Once imported, I went to Opera:boomarks and just had to move around the ones that I wanted to keep and delete the duplicates.