It's a glitch that spellweavers using dryad's allure have experienced for some time. If you abandon them, they go poof. Sometimes this happens when hopping through gates.
In your case, however, after reading the rest of the thread, I think the Ferryman returned to his original form and lost his undead status, thus was no longer subject to your control. Go grab the skeletal dragons from from the Rat Dungeon by Sacrifice Ilshenar.
Also be aware. They don't play well with others. Their wither attack will hit other pets, summons, and players and will start fighting with them. So if you have two of them and sick them on the same creature, be ready for them to fight each other. Keep the all stop macro handy and be ready to invis them.
Having said that, they have a nice hit point leach ability and so are a bit like pet sampires. I make macros to control each one separately and send them off fighting by themselves away from each other. They do quite well unless up against powerful fire creatures like ancient wyrms and greater dragons.
