It seems your local repositories are corrupted or kind of connection problem. The corruption could happen if you unplug the power while performing an update or something like that. I such a case, you could try something like this:
cd /zynthian/
mv zynthian-webconf zwc
git clone -b stable https://github.com/zynthian/zynthian-webconf.git
mv zwc/cert zynthian-webconf
rm -rf zwc
update_zynthian.sh
Regards,