To clarify, the problem is with a link field in the custom content type. I have a custom content type, activity, which has a field containing a link to a PDF. I used BSR to update all occurrences of new.domain.ca to domain.ca when the site went live. But the activity PDF links are still going to new.domain.ca. I did a test and BSR will find and replace the text in another field of the custom content type.
In the database, the PDF is stored in the _wp_attached_file field of the wp_postmeta table as a relative URL, e.g. 2015/07/filename.pdf. It looks like Custom Content Type Manager (CCTM) is using the guid to get the absolute URL, e.g. https://new.domain.ca/wp-content/uploads/2015/07/filename.pdf. That seems to be the only place that still contains any reference to ‘new.’
Can I update the guid to resolve this? I set up redirects in htaccess and this resolves the 404s but I’d like to get rid of all references to .new. I don’t know of anyone using feed readers on this site.