From the owners manual..

NOTE: Only replace the batteries in pairs.
The system may have to be resynchronized if the transmitter
is without voltage for several minutes. To synchronize,
aim the transmitter eye at the vehicle and briefly
press either the Lock or the Unlock button twice. Within
approximately 30 seconds, insert the key in the ignition
and turn it to the ON/RUN position. The remote control
should once again be operational.