I just replaced the battery in my 2001 Subaru Legacy and now the remote on my keys will no longer lock or unlock the car, but the alarm system works when I lock it manually. Is there a way for me to reset the remote with the alarm system on my car?

You gotta change the battery to the remote so it'll send a signal to not set off the

unlock then lock with the key in the door you might need the remote alot of locksmith shops that sell key fobs could help you with that

subaru have 2 security codes one for the key/ignition switch(magnetic code)and one for the remote(rolling electronic) the car is reccognising the key but not the remotes signal to the central locking.
try locking the car with the key then pressing and the holding the unlock button on the remote for 30 secs, see if the car unlocks.if not unlock the car etc....or... put key in door and hold over for 30 secs..etc

battery of car is zapped of energy...not sure if alarm system to blame, after driving it for a few minutes..clock and radio display lights turn off, horn can barely be heard...sometimes, motor shuts down completely. have had to put in 2 new batteries in just a matter of 2 months?...any idea what this may be?

First try to reset alarm by inserting key in drivers door lock and lock and unlock-if this does not work try tail lock as well.

usually after opening the door you can deactivate the alarm by pushing th unlock button or simply insert keyy in ignition and turn it on.

you HAVE to get a remote and unlock the car.the dealer may be able to turn it off with the obd2 system,you have to call subaru.

Subaru Outback Legacy Flashing
Q. I have a 1996 Subaru Outback Legacy AWD manual transmission. the hazards flash when I turn the car off. I tried to reset the system by pushing the little black button under the drivers' side dash but it won't reset the system. I had problems with the brakes so I did not drive it for about two months and when I tried to start the car the battery was dead.
Now the brakes are fixed but the hazards won't quit flashing and the guy who repaired the car said I needed to reset the system by pushing the little black button. And I don't know if I should have it looked at, or change the battery, or if it is something very simple I can fix by my self.
Thank you very much,
Patrick
A. Patrick, you are the third person in the last two days that has come to me with this same exact problem under the same conditions. As of now I don't have any concrete information on this, but I believe the problem to be in the alarm system.
I believe the battery being disconnected or dying does something to the Anti-theft and Alarm System module and having a Subaru dealer reset the system will correct it.
If you do this and it works, please, let me know and I will pass the information on to the others.
Added 11/7/2003
Dear Mr. Ciulla,
I read your Q&A titled "Subaru Outback Legacy Flashing". I recently had the same problem on my 1996 2.5 liter Subaru Legacy Outback and your response is correct but I can give you a little more detail on what worked for me to stop the light flashing (which occurs sometimes if the battery had been dead):
There is a black reset button under the I/P near the anti-theft module.

1. Turn ignition on
2. Hold button 20+ seconds (door locks will lock/unlock 3 times)
3. Turn ignition off

This also resets the key FOB so as step 2.5 you should also press the "lock" button on the key FOB before releasing the black reset button (door locks will lock/unlock one more time--do this with each key FOB you own). That's all!
The questioner in your Q&A said he tried the reset button; I suspect he either didn't turn the ignition on/off or didn't hold it in for over 20 seconds.
PS... pulling the door lock fuse will stop it temporarily if you can't get the above to work and have to take it to the dealer
Regards,
John

Photo Courtesy John Spieth ©2003
Additional Information provided courtesy of ALLDATA

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CODE ALARM SYSTEM
information is always subject to change and correction Used on:
Impreza 1996-2001
Legacy 1995-1999
Forester 1998-2000
Battery GP-23A
Lock: Left button will lock all doors. Double chirp indicates locked.
Unlock: Right button will unlock driver's door only. Hold unlock button app 6 seconds, it will unlock all doors including rear gate. Single chirp indicated unlock.
If the car chirps or lights flash 4x the alarm was triggered.
Panic. Press both buttons to activate emergency honk and flashing lights.
Valet mode: With optional alarm only Press the red alarm button on the left of the steering wheel. The light will quickly double flash. To re-set back to normal mode, press the red alarm light button again

Battery failed and lights flashing?
Parking lights will flash when the vehicle's battery is disconnected and reconnected.
To stop lights from flashing, either:
Press remote transmitter “UNLOCK” button once OR turn the ignition switch to the “ON” position and press programming button for one second (see below).
The vehicle interior (courtesy) light and door open warning light (DOOR AJAR indicator) will then illuminate for 60 seconds when the ignition is turned off, or until the doors are locked with the remote transmitter. Yes, the dashboard instrument panel lights will flash when the parking lights flash.
Programming or Overriding the Alarm when you have lost the remote
Open driver's door.
Turn ignition key to 'On'
Press and *hold programming button* in (see diagram, button under dashboard)
After 15 seconds the the door locks will cycle 3 times. Do not release Programming button
Press lock (left) button the remotes to be programmed. The door locks will cycle one time.
Exit programming mode by releasing Programming button under dashboard and turning key to off.

Code Alarm Programming Button is under dashboard on the kick panel by the driver's left knee, left of the steering column. If you can't find it, it might still be tucked up in the wiring harness higher up in that same general area. The botton is recessed in a plastic ring (see diagram).
This button must be pressed while programming remotes or if the battery was disconnected and the lights are flashing.
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the alarm turned off as soon as you unlock the door with the key... the clicking noise could just be the fact that your battery is dead. hope i was some help