I went through the exact same thing as the OP yesterday with an MX-990.

After about two hours of troubleshooting, I found out that it boiled down to a corrupt CCP file. I did some minor edits yesterday to an MX990 file and something I did (never found out exactly what) messed up the file. I could upload to the remote, but upon reboot it would go to a dark screen and be totally unresponsive.

I had to do the bootloader reboot (ON + MUTE while putting in the battery) mentioned by goldenzrule (thanks!) to get the remote to respond at all before I could load an older file. After using the old file, the remote has been fine.

Just FYI.