User blog comment:IamJakuhoRaikoben/Chapter 477: Transport, Review./@comment-4933386-20160315023949/@comment-7418318-20160315073900

Jacob can probably use it again, but Lucy only said that "Celestial Cage" protected her and Natsu from the spell, without mentioning (out loud) that Horologium needs time to recharge that ability. So unless Jacob's knowledgable about Celestial Spirit Magic, he probably assums that they are permanently protected from his magic.

So from the tactical point of view it would be a waste of time and magic power to try a spell that already failed on them again.

Also he wants to use Lucy as a hostage to pressure Mavis into revealing the location of Fairy Heart, so sending them away would hinder his plans rather than help them.

Of course he could use the spell on only Natsu, but we don't know if the spell allows him to be so selective. Also there's a good chance that he wants to teach Natsu and Lucy a lesson. Considering how he reacted to not getting served a drink, that's quite likely part of his reasons.

I guess there's also a small chance that his spell works on exchange basis and that sending the two to the other dimension will automatically call the ones already there back to him, but I doubt that's the case.