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Car electronics can be very tricky sometimes. Changing the battery in your remote should not cause any need to reprogram your key or remote. I have a trick for you to try:
The old car battery reset trick
I know this sounds absurd, but it works sometimes and is worth trying. If you exhausted all of the options above, disconnect bot terminals on your car battery for 10 minutes. Then reconnect them and try your key fob. This has worked for many people and I have no idea why. If you do, please comment below to explain.
Hopefully this helps out, you would be surprised how many electrical issues this little trick will fix on any vehicle.
It sounds like the disconnect of the battery has caused the anti-theft system to kick in. Anti-theft overrides the key. There is a chip in the key fob and a chip in the ignition lock, if they are paired and both present, the Engine Control Module releases power to the starter and the ignition circuits. When you connected your battery, I am guessing the key and fob was in your pocket.
Disconnect the battery for at least 2 hours. Hold the negative and positive battery leads together for 5 minutes to fully dissipate any residual power. Very important bit, PUT THE KEY IN THE IGNITION, but not turned on. Reconnect the battery. Wait 15 minutes for the system to self check and reset. Start the vehicle.
new battery in fob doesnt mean it cant be faulty retry with a different new battery and or that it is installed correctly -also sometimes a fob will have to be relearned or flashed and that usually means a visit to dealer or service station thats authorized to do so--and if their was rust and oxidation i would recheck and reclean those components again and test continuity
these key fobs go bad often poeple think they just need programing but thats not the case, the board inside the fob sometimes the soider breaks free and doesnt make a good connection, the most common spot is where the battery contact are, take a good look at that area and you may be able to fix it by re soidering it, hope this helps.
On a 1997 civic I had, every now and again the remote would stop opening or locking the car. To get it working again, you needed to open the doors using the key and start the engine. Next time you tried the remote, low and beholdit would open and lock the doors again.
Mine had an ifra red key fob, i.e. the type that has to be pointed in to the interior of the car through the windows before pressing the button, rather than a radio type, i.e. so long as you're within a certain distance of the car, it doesnt matter which direct the key fob is pointing.
First find little notch on side of FOB that will allow you to open the FOB itself. Next insert mini flathead and twist hard until unti snaps open. Hopefully you didnt break it yet. Then pull out circuitboard within FOB. nEXT remove battery and press red button and hold for 5 seconds. Replace Battery then put circuitry back in place. Now, with circuitry in place hold all three buttons while simultaneously pressing the red circuit overload reset button on the board. Then, press the thre buttons in this exact order ( this is a very important step) press the door unlock buttton twice before waiting three seconds then pressing the hood open button 3 times followed by a 5 second delay then pressing lock> But wait, before you press lock you must "chime" this code to the song "waiting for a girl like you" by foreigner. The code will then automatically find your cars code, get married and then you will be in luck - many baby remotes will start to fall from your dash board. If this doesnt work it is probably due to the fact that you have more of a hard rocker or redneck remote and follow all prior procedures but replacethe song with only "welcome to the jungle" or tears in my beer". If this still doesnt work, grab a beer and share it generously with your remote. When this doesnt work, (as I suspect at this point it wont) take your remote and after finishing the 12 pak, take the remote to your local hyundai dealer and threaten to throw up in the main sales room if they dont program it for you. Mae sure you slur the fact that your dad owns Hyundai (even though you are as white as can be) and that you will sue them all out of work if they dont do this for you ...plus you then proceed to puke on the front door handle and tell the customers " this is what you have to look forward to if you get oneof these BEutieeeesss hahahaha" while rubbing your puke infested hands all overtheir nice shirts and blouses, ....this I promise will work. And you should have a nicely programmed remote the next morning after waking up in the drunk tank and the officer gives you a ride home because the mayor of "yourtown" is your neighbor and your supposed to be at home cooking a barbeque for him that after....HIC...that after...HIC that ...noon.