#Docking impossible
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I encountered a similar problem. For me it seemed that the crafts did undock, but were still held together by struts which seem to have reattached and only showed up again after I reloaded the docked Lander and Mothership.
Interestingly, the first undock after reconfiguration in Mun orbit was successful, but after landing and redocking, the crafts stuck together on route back to kerbin.