While re-publishing an InfoPath form/template, if you get the error message below, there is a way around it, but it’s not the easiest solution in the world, but it has worked for me:
Infopath cannot modify the form library template because the file does not exist. Copy the template to the form library or create a new form library.

An answer was given to me through the SharePoint forums and I want to share it here, along with an extra step I found that I needed. Here are the steps:

  1. Open the problem form library with Explorer.
  2. Rename the default template.xsn under Forms folder to template1.xsn.
  3. Copy the new template to the same location then rename it template.xsn.
  4. Browse to problem form library > Library Settings > Advanced Settings > under Template URL of Document Template section, change (or add, as needed) the libraryname/Forms/template1.xsn to libraryname/Forms/template.xsn > Save.
  5. Remove/Delete the other ‘old’ template
  6. Open the template.xsn under Forms folder in InfoPath Designer > Republish the form again.

Now, that being said, what I found is that, having added a few new items/fields on the InfoPath form, when it was republished, all except for two of the existing promoted fields (no new promoted fields with publishing) were not showing in the form library. The way this was fixed was to relink all the records.

To do this, go to your form library and click on the Library Settings icon in the Library tab. There, you will see a link that says “Relink documents to this Library” which you need to click. Once you get there, click on the ‘Documents’ tab. In the Ribbon, in the ‘Actions’ page, click on the ‘Relink All’ icon.

That should do it!