Based on what you tell I don't think my solution will work for you, but just in case I have the same Error from time to time and what solves my problem is to turn completely off my computer (not just hibernating or restarting), unplug the SK, turn on my computer, wait until completely initiated, launch e2studio, recompile the project, plug the SK board and finally go to "Debug configurations..." select the desired project and click the Debug button that appears to the bottom of the dialog window. I NEVER use any other option to launch a debug session because I observed that many times the other options hang the debugger and end up in the error message you mention.
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