This happened a moment ago. http://imgur.com/a/6Rjd6 My ship got wiped got a different pet too the only thing remained was the crew and upgrades everything else is gone. A month ago my ship got the bug where the teleport bay doors got locked by a invincible walls which I removed with a mod since there was no other solution. And today my ship got wiped. No other mods used before besides the ones to help fix the game.