Arkham Horror, Amun Re, R-ECO, Ora Et Labora, Napoleonic Wars
In the next turn, I attacked Hannibal and won the battle. Hannibal retreated in to Insubrians.
You should have left Boii to attack, so the instant you left, the Subjugation was lifted unless you left a CU there to "babysit" the ongoing Subjugation. See Rule 20.6
It sounds to me as though you may be playing something wrong. Did you think that you could attack Hannibal in Verona while you stayed in the adjacent space of Boii? - You must enter Verona to attack Hannibal. If you leave a CU in Boii the subjugation points stay - if Boii is left empty the points are gone.