Re: Losing contact
Try using the cheat "omni" if you have cheats enabled. See if there's a missing warp point or something of that nature that would disconnect your empires.
I would call the fact that your ship is in their system and the lost contact message popping up is buggish and it'd be worthwhile to send your save game to Aaron. Let him know if you are using a custom shipset and which mod version etc.
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