I did not play in multiple windows, just forgot to close kongregate with elements running.
By not closing the window at work, you were effectively playing in multiple windows; one at work, one at home.
The one at work kept its state as it was when you left it, and when you continued there it overwrote what you had done in the window at home.
This has nothing to do with Kong, by the way. It's just that the game only loads a save when you log in, so make sure you start all sessions by logging in or you might lose progress.
There most likely is no way to recover what you've lost, but you can always try sending an email to game.elements@gmail.com. Just don't expect anything.