With our alarm you have to re-learn the remotes with the alarm unit whenever you replace the battery. There should be instructions in the alarm manual as to how to re-learn remotes, but generally the process would be similar to:
1) Set the alarm system into "programming mode" (some kind of ignition-switch on/off pattern or the like)
2) Press the lock/unlock button of each remote in turn to tie it with the system
3) Return the system to "arm mode"
Obviously it will be different for each alarm manufacturer, but the theory is most likely to be similar.
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