Mis-step in modifying Arduino (used in my core memory loader)

RATIONALE FOR CHANGE

It is desirable to have the core memory loader power up and down with the 1130 system in which it is installed. It is supplied with 12V from the system, then the shield I designed drops and regulates the voltage before powering the Arduino and digital logic on the shield. 

This loader communicates with outside systems or terminals using serial communications over the USB port of the Arduino. The design of the Arduino will take power from either an external supply (e.g. my shield) or the USB connection. This means that when the 1130 is powered down, if the USB is still connected to an external system the core memory loader will remain partially powered up. 

What I want is to be able to use the USB link for communications, also to update the loader with new code for the Arduino, but not to power the Arduino if the 1130 is not powered up. I looked for information about how to accomplish this and found an article suggesting that I remove the polyfuse on the Arduino to cut the power from the USB port. 

Pads where the polyfuse was installed

Polyfuse - a resettable fuse

What this accomplishes, however, is to completely shut down the USB port, not just for power delivery. Time to reinstall the fuse and work out a plan B. 

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