Aye, sometimes this can happen and you'll have different realms owning chunks of a county long before you holy war. I'm a little shocked it still hasn't be addressed... you can holy war for the entire county, so long as the capital is held by a heathen. Same with de jure claims in general... had an instance in a game a while back where England held two chunks of some county in the Duchy of Leinster, but only the city and the bishopric. The capital barony and the county itself was property of my direct vassal, the Duke of Leinster.
So had England held all of the county, I could've pressed a de jure claim for the whole thing for my vassal. But instead we had to fight two wars to gain only a holding at a time. At the very least, we need to be able to press a "County Claim all in County X" CB. I'm cool with not being able to press every single county claim at once, but we should at least be able to reclaim a county at a time.