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Is it rules legal to run a thunderhawk with a chaos army in apocalypse?

It's rules legal to combine whatever armies you want in Apocalypse.

The Apocalypse rulebook gives an 'Allies Matrix' that breaks down the most likely alliances in order of likelihood... but it's only intended as a guideline (and says as much). In practice, you can plonk down on the table whatever you have.

You can run a thunderhawk - there is a boxout in the Apocalypse book stating that Chaos can use any normal SM formation, which includes thunderhawks