Hey!!
The following troubleshooting steps might get your Harmony Remote working again!!! It is what the Logitech customer care gave me to do and it worked perfectly!!! Hope it works for you too!!!
1) Remove the battery from the Harmony Remote for 10 seconds and reinsert it. If this does not resolve the issue, please continue troubleshooting.
2) Ensure you have the latest version of the Harmony Remote Software (7.7).
3) Update the firmware on the Harmony Remote. The following link shows how to complete this task:
http://logitech-en-amr.custhelp.com/cgi-bin/logitech_en_amr.cfg/php/enduser/std_adp.php?p_faqid=107474) Try putting the Harmony Remote in safe mode and complete the firmware update again. The following are the steps to accomplish this:
a) Remove the battery from the Harmony Remote.
b) Press and hold the power button while reinserting the battery into the Harmony Remote.
c) To get out of safe mode, remove the battery for 10 seconds and reinsert it into the Harmony Remote.