I found, buried in a technical manual, the following rules for working with electrical systems on modern ag equipment. According to the experts:
-Never disconnect the batteries of a machine with the key switch "on." Disconnecting batteries can send voltage spikes through the system if the key switch is "on." The computers in modern farm equipment do not like voltage spikes. In fact, voltage spikes have been known to "kill" pricey circuit boards and computerized components.
-Don't connect jumper cables while the key switch is "on," for the same reason: potential voltage spikes.
-Do not connect or disconnect electrical connectors/wiring harnesses while the key switch is on or the machine is running. I've had numerous in-the-field precision farming technology experts assure me that it won't hurt to disconnect a yield monitor, header height control system or planter wiring harness while the system is powered up, and I've done it dozens and dozens of times. But the experts at the manufacturer say it's best to kill the system before connecting or disconnecting wiring connectors. My understanding is that there are robust electrical systems that aren't bothered by "live" connecting/disconnecting, and there are more delicate systems that can be harmed by voltage spikes that may occur during those procedures. Unless you're very sure what sort of system you're working with, play it safe and turn off the ignition switch.