I decided to delete a custom post type and change them to pages instead. The pages display properly but anything in the directory that the custom post type used is returning a 404 even though the pages display normally.
Here is an example
Every page in the /accidents/ subdirectory is returning a 404 even though the page is displaying the proper content.
I deleted all of the posts with that posttype out of the database but I think I must be missing something.