The Voyager 1 lost speed gradually after gaining speed from gravity assist. Is the external thrust applied in the opposite direction to move closer to the planet, or does the spacecraft lose its momentum after the sudden rise in speed?
Additionally, the probe has just passed a large planetary body with its own gravity well. The probe has to climb up out of that planet's gravity well which costs momentum.
There is a net gain in momentum overall, the probe is leaving with more momentum than it entered the slingshot manoever, but the highest velocity is about where the probe is moving parallel to the planet's surface.