Plugin not working since /wordpress removal from Site URL

I have removed the “/wordpress” portion from my Site URL, and now my plugin is not detecting the cold/static links that were not updated automatically when the change went through. It did detect all of my pdfs in my pdfs folder out of the root folder of wordpress, so I simply moved those into the wordpress folder and that fixed that. But I have several pages with cold links that have /wordpress still in them, and they are not being detected. Is there something I need to configure in the “Look for Links In” section of the plugin for the search to detect these new broken links? I need a solid number for how many links broke so I can guesstimate the amount of time it will take to fix them.