As you suspect, unless you installed one or more of the files, that command can’t be related to your keyboard being gone.
Something else must be the reason.
Did you install or uninstall any other software?
What do the following commands say?
systemctl --user status maliit-server
systemctl --user status xt9-server.service
But I guess in order to revert the installation, so something like:
devel-su
for pkg in feature-xt9 jolla-keyboard-settings-xt9 jolla-xt9 jolla-xt9-cp jolla-xt9-server patterns-sailfish-xt9
do
pkcon remove $pkg
done
pkcon install feature-xt9