Nano Serial Port Failure

I've gone through a lot of Nano's. What usually happens, is that eventually, attempting to upload sketches over the USB port simply fails. However, I am usually able to upload sketches using a USBASP programmer. And until today, I wasn't really able to establish a specific event that might have caused the Nano's serial port to stop working.

What I think might be happening, is that when I have the Nano connected to other circuitry which has a different power source, it might be causing the USB port to fry when I connect the USB cable to the nano.

When I build my circuits, if I have, for example, a separate ESP8266 in the circuit, I have to power it from 3.3 volts, so I will incorporate a linear step-down power converter that I will set to roughly 7 volts, then I will have another regulator step that down to 3.3v while connecting the 7 volts to the Vin pin on the Arduino.

OR, I might have a circuit that has an external 5-volt power supply which I will connect to the nano's 5v pin, while also using it to drive external LEDs or maybe even an IR input receiver.

No matter what the case, it does seem that when I have the circuit powered up externally, then I connect the USB cable to the nano to upload a sketch modification, what eventually happens is that the ability to upload to the nano over USB simply stops. The USB port registers on the computer (sometimes), but avrdude can't talk to it, so I have to resort to using the USBASP programmer.

So my question is: Is there a prescribed method of connecting the nano to external power sources such that doing so will not in any way interfere with its USB communications so that I can plug a USB cable into it while it's powered externally without causing any problems with the nano's USB abilities?