"'I'm not surprised.  You just told dnf that /home was its working
directory, so it can do whatever it wants with it.  It's going to want
to clean it out so only the relevant files are there."

Sorry, I did not give dnf the right to delete files it did not create in that directory.    Note that it also wiped sub directories, which I did not agree to. 

Here is what the man page says:

" --downloaddir=<path>, --destdir=<path>
             Redirect  downloaded  packages to provided directory. The option has to be used to‐
             gether with the --downloadonly command  line  option,  with  the  download  command
             (dnf-plugins-core) or with the system-upgrade command (dnf-plugins-extras)."

No warnings about wiping other data !