Because both config and world were moved to /var/lib/portage in 2.0.51, syncing the portage tree now removes both those files, if PORTDIR is also set to /var/lib/portage.
I know that having PORTDIR=/var/lib/portage is not the default and supporting all possible PORTDIR values would be counterproductive, but still please consider adding the following patch to portage.
Created attachment 43010 [details, diff]
Patch to protect config & world files during emerge sync
The patch protects the config and world files during emerge sync and doesn't
affect anything else.
/var/lib/portage is for "private" portage data. There will more than likely be more things added in the future, which would require further and further expansion of rsync's "except" clause. Furthermore, it might be possible that names could even conflict..