Just cycle all the cyl in your tractor hyd system several times.
Actually, just because you changed a BH cyl, there is no reason to think air was injected into the system. The fluid from the BH should have gone to either 3pt, or tank.
If you think your pump is sucking air, look in the hyd tank with a flash light and see if there are lots of small air bubbles. Also allow some time for the air, if any, to settles out, and check again.
If you continue to have air in your system, recheck all the suction fittings, and pump flange.