The battery in the Clip doesn’t suffer from partial charging. So feel free to simply disconnect (and only partially recharge) when your transfer is complete.
But what type of battery does the phone use? The Clip uses a Lithium-ion polymer battery. If the phone uses a Nickel-cadmium battery, I can see where you could have charging problems with it. They can develop memory problems.
The Clip’s battery is not like that of your phone–partial charges are fine with this newer generation of battery, which does not suffer from the infamous battery memory effect.