I have a Hampton Bay universal remote that worked great until I had to change the batteries. Since I replaced them, the remote turns seems to work but does not appear to be relaying a signal to the fan or light. All of the toggle switches in the remote match up to the fan itself. Is there a button combo on the remote that I have to input whenever the batteries get changed? Any other ideas would be great as well.

Nothing special to do when changing the batteries other than to double check that you installed it correctly, start there. I would also move all dip switches in both units to ON

Honestly I don't have any information about reprogramming universal remotes, other than the dip switches, which you have covered (make sure they are all properly seated).

Contact the manufacturer and see if they can help you.

Ceiling fan remote controls - help and FAQ- Ceiling Fans N More (http://www.ceiling-fans-n-more.com/ceiling-fan-remote-controls.php)