Yep, I followed this thread on how to reprogram my code from bare metal. In practice I didn't need to re-flash the keys though, and it brought it back from the dead.
Since then I had one issue where the CC3000 just wouldn't connect to my WiFi network, that just simply running the CC3000 patcher has brought it back. You might want to try that step first? You can patch your CC3000 and reflash your Core in DFU mode without the need for a STLINK V2 JTAG programmer.