I think you're saying that you want to have a PC monitor an Arduino to confirm that it is running, without powering the Arduino from the PC. I assume you want to avoid snipping USB power lines.
Connecting via FTDI instead of via the USB port seems like a good option, if you have a suitable adapter.
Another option is to set up a serial connection from the Arduino under test to a monitoring Arduino; the purpose of the monitoring Arduino would be to detect when the Arduino under test stops communicating. It is up to you whether the monitoring Arduino detects the 'death' of the test subject itself, or merely passes communications through to the PC and have the detection done there. It is up to you whether you want that communication to include any other data such as battery voltage/status from the test subject.