I fixed this by deselecting and reselecting the Fenix in the seated passengers tab of the FSDT Installer, AFTER installing the new livery.
That's what the manual says at page 98, where all cases of missing passengers are discussed.
Now, deselecting/reselecting might not always required, most of the time it should be enough to enter the Config page and let the list refresh but, depending how long ago you enabled seated passengers, you might also need to deselect/select again, because it depends which version of the airplane and the FSDT installer was used to enable seated passenger last time.
In theory, after version 3.1.7, where the installer patches the files as suggested by Fenix, you shouldn't have do deselect/select again after you did it now but, after installing a new livery, you'll always have to at least enter the Config page, and let the list refresh all planes.