There are two separate harnesses that connect to the WPC DMD controller board. The low voltage connector on the bottom left side of the board powers the logic section. The high voltage connector on the bottom of the board powers the DMD. They are often zip-tied together.

We recommend removing the high voltage harness to prevent live wires from shorting against you or anything else in the machine. Alternately, you could just unplug it but there's some risk that the connectors on the harness may bang into something they shouldn't. It's safer/cleaner to remove it from the backbox.

The one on the bottom with the orange wire. When in doubt, you can match up the colors of the wiring to tell which connector goes to the old DMD.

Nothing wrong with pulling fuses. But you still need to make sure the connectors on the unused harness don't accidentally short anything.