The update was not successfull, because of the host.mk files and the configuration files below ~/etc/check_mk/conf.d/ are the foundation for what is shown in the GUI. Wato/Setup reads and writes these files. If these are broken, nothing will work correctly.
Maybe that you are having multiple problems, but this has to be fixed first in my opinion until the cmk-update-config runs without errors. After that, we can analyse the other problems.