Do you have Uplay Cloud enabled? It has been known to cause problems with saved games for people

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Next time Uplay opens up. Goto settings and uncheck "enable clould save syncronisation for supported games"
Close the UPlay launcher again and then re-launch it to make sure changes have taken affect and then try launching AC2. You may get lucky and find yourself back where you should be as it loads the save from your computer instead. If not. Just see if it solves the problem of losing progress at least

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