You can just unplug it.
As long as you are not uploading a program at the time nothing will be damaged on the Eleven.
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I have a system of remote PCs that run a special build of Windows XP that each connects to two 'Eleven' arduinos. This was built in 2012. The problem I have is this. I need to replace some of the eleven's. I can't get the same model of eleven. The ones I used had a mini USB connector, not a micro US...