What does it mean when my Hunter energy star model 44110 thermostat has a message on it :"RE CO" while my air conditioner is running.

It is nothing to worry about, it is what they refer to as "auto recovery mode".

It just indicates that the difference between the current temp and the next programed setting is larger, and may require the unit to run longer.

This setting supposedly causes the unit to run a little extra so that when the next programed temp time arrives, it won't have to work so hard to reach the new temp.

I believe you can disable this function by removing the unit from the wall plate, and locating the switch on the back of the thermostat.