I have a similar type issue.
I have a template published on one SharePoint server. We made edits to the form as an upgrade but will be publishing it to another SharePoint location on the same server. We need to move the historic XML files from the old site to the new site and have them link to the new template.
The first thing I did was published the new template over top of the old site. This updated the xml files with the new fields and formatting. so now the old data forms look correct.
Then I turned around an published the new form on the new sever.
Here is the issue. You can't simply copy the only XML files to the new server in the form library... the "mso-infoPathSolution PIVersion href=" still points to the old SharePoint site.
So when you open the xlm files you are still linking back to the old template.
The second you delete the old site the xml files will be unable to connect to a template.
How do I successfully connect the old xml files to the new template on the new site without manually editing 800 plus XML files =/