WordPress: Fix broken links to custom post type pages

We have a WordPress site that was hacked. We rolled back the server to before it was hacked to remove the virus. Everything is fine, but a custom slideshow on the homepage and sidebars that have thumbnails that link to custom post type pages, are no longer linking to the pages, but instead giving 404s which result in a redirect to the homepage, as all 404s do. You need to fix the site so that the thumbnails again link to the custom post type pages properly.