I suspect https://github.com/vim/vim/pull/6970 and related https://github.com/vim/vim/issues/4405
Basically, before the patch it was impossible to put vim into full "default colors mode" as there were no way to do it -- :hi link survived :hi clear. Also cleared highlight groups were impossible to set with :hi def groupname ....
I guess that ...
As it turned out, I was running an older version of Vim. Updating using the following "three-liners" solved the problem.
sudo add-apt-repository ppa:jonathonf/vim
sudo apt update
sudo apt install vim vim-gtk3