Interesting. I found a faster solution than deleting all the queries and re-adding them. You can just select the "Version" of the query from "Latest Version" to the latest date there is, save, and then the reference is updated. You can toggle it back to "Latest Version" if you like. So it looks like "Latest Version" did not update to the actual latest when I had a new version of the query. So I believe that when a new version of a query in a library is created, it should trigger an update on all apps that are tied to that version.
Edit: be advised... that can potentially put your app in a permanently broken state if you have a trigger with a redirect and that was dependent on a query. Good thing I made backup copies of all my apps or I would have lost two of my apps.