We’ve had this issue before and it seems to be a bug with the SAM-BA programming application.
The only workaround we’ve had is to try to use another computer to perform the firmware update process.
Are you updating to the bridge firmware or to the regular Ciholas firmware?
If you’d like to update to the recent Ciholas firmware, you can use the Device Firmware Update (DFU) utility from the website.
Thanks,
Jawad