I'm trying to create bookmarks that will work in a PDF

I think that bookmarks can point to either pages or to text anchors. If you go to the Window -> Interactive -> Bookmarks panel, you can see it in action. First, make a boomark with nothing selected - it creates a bookmark to your current active page, and the icon in the Bookmarks panel is a page icon. Next, make sure your Type -> Hidden Characters are turned on, then click into some text using the Text tool, and when you click that "Make Bookmark Here" button, it creates a text anchor:

 So I don't know anything about the construction of your cookbook, but I don't see any real need to ensure that both bookmarks are the same type. If they point correctly - if you can click on 'em in the Bookmarks pane and get taken directly to that location in your InDesign file - then they're fine. If they don't point correctly, or if you need them to be all set up as page references with no text anchors, you can simply trash 'em and make fresh ones, I imagine. 

Likewise, if some of them aren't working, you can trash them and make fresh ones. If you didn't know that text anchors exist, and you didn't have invisible characters turned on, and you made text edits, that may explain why some of your bookmarks don't work. You may have accidentally written over some of those zero-width invisible text anchors?