The second conflict on the world of Iridonia occurred during the Jedi Civil War. This war pitted the Galactic Republic against Darth Revan's Sith Empire. The Republic forces were victorious in this particular engagement on Iridonia.
The Essential Atlas is the only place where the Second Battle of Iridonia is mentioned. The precise timing of the battle is not specified; it is only represented graphically on a galactic map. The initial battle at Iridonia is also shown on the map, depicting a Sith triumph. This first battle is described in the Wizards of the Coast supplement "Iridonian Darkness" (original article link) on Wizards.com (content now obsolete; backup link). It's placed early in the war, around 3958 BBY, after the Telos IV bombing. The exact time of the second battle remains unconfirmed within established canon.