Thank you Fabián for reporting this.
The footer.php and header.php were moved to a subdirectory /include/templates/, but this directory was not added to the Makefile target for creating the .pot file. As a result, all translatable strings from the header and the footer were missing from the PO template file.
I fixed the Makefile and uploaded the new .pot file to Transifex. Those strings should now be translatable again. Unfortunately, all translations for those strings were lost as well. I'll recover those translations from saved .po files.