While working on cleaning up my automation around my rocket while it was in space, I attempted to deconstruct automation wires and gates (in automation view) on the same tiles as the rocket's automation outlet, and shortly after I opened up the starmap to find that my rocket was gone. It looks like the command module got deconstructed while it was invisible/in space. The duplicant got freed, but the rest of the rocket remains invisible. I'm not sure if the automation step is required to deconstruct it, or if you can simply directly deconstruct it. Either way it seems like it should not be possible.
Deconstructing automation on the same tile as the command module queues the command module for deconstruction while it is in space.