We had a new battery put in our 1999 lincoln navigatior and the rear air suspence went down and we can not get it to to fill back up

You will need a special tool for the back brakes,Autozone will loan it to you for 60 bucks,you will get it back when you return,I used it.I replaced brake pads front and back and both back rotors.The driver side rear had metal on metal,all disc brakes,brake pads on that rear side were completely worn down to metal,the driver side was like new,kept wondering why,replaced both rear rotors,put back together,then then I noticed where brake line hose went into brake caliber was leaking,so that caused the side with new like brake pads not to be gripping disc putting all brake pressure of that one side,so the copper fitting their was bad,put new one on and leak stopped.

air bags solenoid is stuck open releasing air this happens when you raise then lower car in normal working mode valve opens closes as need to maintain ride hight when car is jacked up it thinks the bags have been filled emtys bags when you lower car down to readjust height you need new bags and a new compressor it will burn up trying to fill fill fill when it cannot suncore industries around 370.00 for everthing 2 to 3 hrs to replace

I was sitting at a stoplight. The other day in my rear airbags went out and now they won't fill back up with air. Does anybody know what the problem could be the airbags don't look dry rotted, or look like they have a hole in them

You will have to turn the air ride system off until the bag is fixed. Otherwise the pump will run continuously trying to fill the bag. This will obviously kill the battery.

I had this problem last year with my LincolnI. I took it in and for 200 bucks I had to replace a wire that went out of my air suspension. Right after that it drove smooth again.

It's the bags

You need a compressor that will put out 200 psi. Here is a new one on ebay for $212 http://cgi.ebay.com/ebaymotors/1998-1999-2000-Lincoln-Navigator-Air-Ride-Compressor-/230481832909?cmd=ViewItem&pt=Motors_Car_Truck_Parts_Accessories&hash=item35a9c9abcd#ht_1913wt_1167 Here is a used one for $119.50 http://cgi.ebay.com/ebaymotors/1998-1999-2000-LINCOLN-TOWN-CAR-AIR-RIDE-COMPRESSOR- /170491628713? cmd=ViewItem&pt=Motors_Car_Truck_Parts_Accessories&hash=item27b217cca9#ht_3365wt_941 Another option is to convert the system to springs and shocks. The conversion kit will cost $327. http://www.strutmasters.com/Lincoln-Town-Car-Air-Suspension-Conversion-Kit-p/-ltc-r2s-4.htm

It's listed here as a 98 lincoln and a 99 exepedition.
I'll go with the lincoln, as this sounds like an air suspension problem. First, check the system shutoff
switch, inside one of the side panels in the cargo area.If for some reason it is off, turn it on and your all
set. If it is on, with the key in the on position listen
under the hood for the compresser working, if it is working, listen at the rear of the car for an air leak.
If the front end is up and the rear suddenly went
down, odd's are there is an air leak. possibly a blown air bag. Hope this helps. Good luck.

Perhaps the rear height sensor isnt secured or plugged. Check the ball stud mounting bracket to be sure its tight as well.

I had a 1999 Expedition. When you put the 4x4 on it raises the vehicle an extra inch or 2.
It may help to turn the 4x4 off. Two wheel drive is a lower air setting.
Your original pump may still be good. The problem can be in the front. The compressor is not filling the front suspension to the cutoff point. It will lift the rear after the front end is at running height. Since you lost the front end first, the remaining air bled out there and then the rear came down. Once you shut down the car the suspension was done, all the air was let go.
There are adjustment solenoids on the body but you need someone qualified to repair this.