I have previously cleaned my Canons sensor manually. My 5D Mk3 is greyed out on manual clean. How do I get this back into operation?
Page 293 (it is on page 299 in the manual for firmware version 1.2.0 and later) of the EOS 5D Mark III Instruction Manual indicates that if the battery grip with size AA/LR6 batteries is attached manual sensor cleaning will not be possible.
If you are cleaning the sensor manually and the battery gets dangerously low, a beeper will sound as a warning and page 294 (page 300 for firmware version 1.2.0 and later) warns you to stop cleaning the sensor. Although it is not explicitly stated in the Manual, I've heard anecdotal accounts that when the LP-E6 battery is very low the camera will not allow manual cleaning.
The reason battery power is such a concern is that the current from the battery holds the shutter curtains open and the mirror up while you are manually cleaning the filter stack on top of the sensor. If power is lost the mirror will drop and the shutter curtains will close. If there is an obstruction in the camera, such as a cleaning swab or the nozzle of a blower brush, the shutter curtains and/or the mirror mechanism could be damaged when they strike the obstruction.