After running freebsd-update to upgrade from 12.2 the 13.0, the xfce4-settings application disappeared. Installing the package fixed the problem.
Either this didn't used to be a separate package, or it got dropped from the xfce meta-package at some point.
It seems strange freebsd-update has removed a port/pkg or files from /usr/local, those are managed by pkg.
Maybe this happened due to pkg upgrade run afterwards?
do you have some log about the event? Maybe some information can be gathered from /var/log/messages? pkg with default configuration logs it's actions there. Maybe for some reason pkg decided that package needed removal?
Without some further details it's very difficult to understand what is going on.
Apr 14 11:21:55 shawinigan pkg: xfce4-settings-4.16.1 deinstalled
It looks like the the "pkg upgrade" run as part of the final reinstall of 3rd party content decided to remove it.
Actually, digging further, the "xfce-4.16" meta-port was also deinstalled, but othewise all of xfce is still here. Running
pkg install xfce
Didn't tell me xfce-4.16 was already installed, but it didn't actually install anything either.
Normal that the rest of xfce survived, the xfce port is just a meta port, it only defines dependencies which can remain.
I have no idea why pkg upgrade decided to remove those ports. My only suggestion is to keep an eye on pkg upgrade and checking what it tells you before confirming the operations it proposes. It usually also gives a reason for it's decisions. Maybe it detected some conflict.