I haven't tried this (and don't have time right now) but since the error is about combining the armies, try removing the army entry from one of them. Like this:

character Flavius Julius, named character, leader, command 0, influence 0, management 0, subterfuge 0, age 47, , x 89, y 82
traits GoodCommander 2, NaturalMilitarySkill 1, GoodDefender 1, PoliticsSkill 3, GoodAdministrator 2, Austere 1
ancillaries aged_retainer
army
unit roman generals guard cavalry early exp 1 armour 0 weapon_lvl 0
unit roman hastati exp 1 armour 0 weapon_lvl 0
unit roman hastati exp 1 armour 0 weapon_lvl 0
unit roman triarii exp 1 armour 0 weapon_lvl 0
unit roman archer exp 1 armour 0 weapon_lvl 0

character Lucius Julius, named character, heir, command 0, influence 0, management 0, subterfuge 0, age 31, , x 89, y 82
traits GoodCommander 1, PoliticsSkill 2, GoodAdministrator 3, Energetic 2
ancillaries freeman_clerk