Yes, un-attached parts self destruct when you start. Its likely those parts, or the parts they were attached to, where not attached to the body of the mech. Clearly I need a more tolerant snapping distance and more obvious connection feedback.
Alternatively, I did consider allowing you to build mechs with disconnected parts that would either stay in orbit around the cockpit or lay where ever you left them. This might lead to interesting turret or mine laying tactics
Thank you for the feedback.