I have a seneca 3. My problem started out like that, easy to sort of fly
with. Then it got worse. Sometimes wouldn't at all retract, or just
partially then pump would go off.
We, flushed out and changed fluid, swaped up and down relays(they are
the same), measured pump pressure, changed pump/motor, gear was in no
way binding. The last thing checked was an over pressure limit switch
that was going faulty and shutting the pump off.
2000 Saratoga? Mmmmm, nice.
Our gear is probably similar in design?? Good Luck.

John, which engine on the Seneca drives the hydraulic pump?