Remove all power from the furnace, it is likely the brain in the furnace is need of being reset, from the battery replacement, why did you change the battery, was there an indicator telling you to change it?
Many times just removing all the power to the furnace will do the trick with a reset, if not let me know and we will go from there, but it sounds like the main brain is confused or bad, more likely confused, so try the power removed first.
Than let me know
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