Connect / disconnect USB while external power source remains connected
An answer to this really requires some more information about your data collection system. Is it designed to be able to be powered from the host USB +5V connection?

If so then the proper operation of the target device demands that there be an appropriately designed circuit to gracefully switch between the external power and the host USB 5V power. 

If you have the data collection device properly designed with decent bypass capacitors in place along with a good ground system then it should not be a problem to plug and unplug the device whilst its external power is applied. This scenario is not any different than when you plug an externally powered USB hub up to your computer. 

I would discourage you from making a setup that demands use of a USB cable that has had it's +5V wire cut. Someday you or someone else will forget and plug in the device with just any handy USB cable and then damage may ensue.