Unfortunately it seems that many people are having this problem. Apparently it has occurred to people after a Uplay update. From what I understand the only possible help is if you have Windows 7 or 8 and have Windows Backup enabled. If so go to C:\Program Files (x86)\Ubisoft and find the folder named Ubisoft Game Launcher. Right-click it and chose Previous Version. If it is there, open it and drag the save game folder to your desktop. Click the Restore button. Then navigate to C:\Program Files (x86)\Ubisoft\Ubisoft Game Launcher and place a copy of your savegames folder in it.
Sounds like in the future you should regularly backup your savegames folder. I would also like to note that I found this fix on the internet and have not personally used this method.