I finished the main line, low-power tunnels, the winter games, found the first wormhole, got 2,000 power cells, completed a dozen different paths, and then I loaded it up again and it was all gone. My Kong acheivements were there, though.
Your save file is tied to your computer, not your Kongregate account. You can lose it if you clear history, or use private browsing, or even just switch computers.
 "Run 3"){kind=icon}
Your save file is tied to your computer, not your Kongregate account. You can lose it if you clear history, or use private browsing, or even just switch computers.