transponder stopped working

i had my battery disconnected for a while a few days ago installing a fuel filter on my Acura Integra, and afterwards my transponder remote for my Clifford Matrix RSX 3.5 no longer worked.  None of the buttons work, for either the alarm or convenience functions, yet i am still able to enter valet mode and my domelight supervision and ignition controlled doorlocks are all still working....so i know the alarm brain is getting power and al that, it seems like the code hopping got out of sync, but i tried what Clifford suggests of repeatedly pressing LOCK on the remote to re-sync it, but to no avail..any ideas?

replace the remote battery and then unplug the antenna on both ends.  then plug it back in.MECP certified installer