I have a client installation, using 4.7, with a semi automated deployment system for changes to master pages, UCs etc. using a batch file.

When I run the deploy (which copies over the masterpages, scripts, ucs and binaries to the directories of the staging and live boxes) the Umbraco database seems to lose the link between the document type and the template for certain doc types only and I have to manually set them up again.

Any idea what could be causing this or what I could do about it?