As described here: https://www.simplerockets.com/Feedback/View/wi48aZ/Rocket-Command-Control-issues
- EVA astronaut from primary command pod
- "Enter" chair on secondary craft w/ Command Chip (connected via docking ports)
- Undock secondary craft
- Attempt to take control of secondary craft.
Selecting a part on the seconadary craft and hitting the "select command pod" button selects the command chip in the seconary craft, thereby making the "take control" button available.
When you hit the "select command pod" button in selects the command pod on the primary craft.