Since you pruchased from the website I'll assume that you bought it via Humble and not via Steam.
If you linked your purchase with a humble bundle account you can log in on their website and go to "My Library". There, just download the game again, it'll be the newest version.
If you haven't linked your purchase you need the link that was originally sent to you via email. That's where you downloaded the game the first time. Just download it again, that'll be the newest version. You might also want to link your purchase with a humble bundle account now, it will make updating easier in the future.
Either way, to keep your built machines and what levels you completed, copy the "Saved Machines" folder and the CompletedLevels.txt file from the old game folder to the new one.
This is a long shot, but it's worked for some people. Go through your history and search for a humble bundle link... The link should be like humblebundle.com/ (something random with lots of letters...) or something similar. It may take some trawling through your history (assuming you haven't cleared it since you brought it...) but if you do find it, theres also a steam key you can use as well.
Good luck, if this fails, then we might need to bring Von in...