They will have to program the new sensor ID's into the Wireless Control Module (WCM) to get the message to go away. I would highly recommend you replace all the sensors so you won't have to endure this issue multiple times. If the battery went out (or you had another problem) on one, the others are probably close behind, especially now that your vehicle is a little over 8 years old. I replaced all mine on my 06 recently when I got new wheels/tires. I had the same problem most are having with the 05-07's.
The problem is with Chrysler/Jeep. The idiots programmed the ID numbers of the original sensors into your Wireless Control Module (also known as SKREEM module) at the factory. They are stored in the non-volatile memory, so the only way to get it changed is go to the dumb a$$ stealer and have them charge you mega $$$ just to change the ID No's in th WCM. You're right though, the new sensors will all work fine, but you'll get that message forever, unless you change the ID's on the new sensors to the ones that were on your original sensors.....or pay to have the ID's in the WCM to reflect your new sensor ID's. Talk about stupid!!
What I have done is purchase Dorman cloneable sensors (all of theirs are now suppose to be) and their cloning tool. You can purchase it as a kit. It'll work on all Dorman sensors (315 and 433 mhz) that are cloneable. Just get the ID's off your original sensors (you can get them read at any tire shop, or buy a reset tool), clone them onto the new ones and your light will go away. I, personally, refuse to go to the stealer and have them fleece me, solely because of their stupidity in designing the system. If you want, go to the dumb stealer and ask how much it'll cost for them to do it for you with their StarScan tool. Add in you inconvenience and hassle of taking it in, and then deduct that from the cost of the kit (again it'll work on all Dorman cloneable sensors) and that'll be your real cost.
Edit: If you don't have the old original sensor(s) you'll have to either go to the stealer and have them get them off the WCM with the StarScan or find someone with a diagnostic tool (such as a Autel MaxiDas DS708) that will read them.