Hernandez has moved to Pramac Ducati for the rest of the season in place of the injured Ben Spies.
Australian rider Cudlin takes Hernandez's place alongside Michael Laverty in the PBM line-up.
The 30-year-old is currently second in Germany's IDM Superbike series.
Cudlin made a couple of MotoGP appearances in late 2011 as a substitute rider.
He was called up by Pramac for Motegi after Loris Capirossi suffered a dislocated shoulder at Misano, and impressed by running 12th before crashing out of the race.
That performance prompted Aspar to recruit Cudlin for the next round at Phillip Island, as its regular rider Hector Barbera had been hurt at Motegi.
But Cudlin did not get to start his home grand prix as he had a heavy crash of his own in practice.
He had a couple of races in Moto2 the following year before departing the grand prix paddock.