I installed rkhunter from source (1.40 I think) and then later updated to 1.4.2 from source (as there is no app update function in rkhunter and the latest version in apt is old) however that means I have the old version at /usr/bin/rkhunter and the new at /usr/local/bin/rkhunter. As long as I remember to use the right path (or ensure /usr/local/bin is higher in $PATH) it seems ok, but I'm not sure having two versions of the rkhunter at the same time and using the same config file is a good idea. So! Is there a way to remove the old and keep the new and not mess up the config?
Best I can think of is backup the config, remove with apt, reinstall for source, restore config and run --propupd to set the database