Scratch that, modifying the ownership of those folders worked indeed, but yesterday I have restored a backup and today the server updated again. And now I have another issue… by fixing ownership those errors go away, however now this error appears
nginx: [emerg] the shared memory zone "domain.com" is already declared for a different use in /etc/nginx/conf.d/fastcgi_cache_pool.conf:
I found this other article in the community forum FastCGI cache error and followed the steps in there, but it did not help unfortunately…