3G or 3GX?
Loading new software in the FBL controller won't make your gyro all of a sudden work differently.
Whatever puts it in heading hold prior to the upgrade will continue to put it in heading hold mode after the upgrade.
Reversing the gyro won't fix it, nor will reversing the rudder channel. That ONLY affects which way the servo moves when you move the rudder stick, or turn the nose of the heli. The same is true for reversing the correction direction of the gyro.
Heading Hold/Normal mode are controlled by the GAIN setting at your transmitter.
If in doubt after an upgrade, go through the FBL setup procedure again. It doesn't take long, and you will know what you have in the end.
* Making the World Better -- One Helicopter at a time! *