Setting the clock on this radio is not done in the software. This option is handled from the face of the radio with instructions found on page 69 in the manual. You really don't want the programmer to reset the time to something from the last time you set it. If you do set it manually, it is not changed during programming.

Alternately, you could remove the clock display from the face of the radio. This change can be done in the Radio Settings of the programmer. Click Settings | Radio Menu Settings | General tab - set the Sensor Display to "Off", save the settings and resend the file to the radio.