We migrated an application from one server to another, and it lost the link to the Template source file for a Document Template Field. This would normally be no big deal, as we can just add it again; however, we didn't know the file was missing. As a result, when we published and installed the application, the template did not install, and the Document Template Field lost it's value for all existing records. When you generate the application tree, the missing file is not noted as a problem with the application setup.
Are you referring to the "Default Template" setting on a Document Template field which loses the template association, or are you referring to actual records (seed records) which lose their selected template in a Document Template field. A screenshot would help clarify for this (feel free to email it to me directly if you have a chance)