Google's back link reporting is notoriously unreliable, some would say absurd. Whatever term you prefer, in any case it's not useful for finding out how many sites are linking to yours. Typically Google displays only a fraction of the back links it knows about.
Most likely, your back links are still there and Google just isn't showing them. 1300 links disappearing all at once would be rather unusual if you obtained them in a natural way. However, if you participated in a shady link exchange scheme (just a theoretical possibility, no offense) and the entire network was banned, then it could happen.
How do you know for sure? Check your site's rankings for your most important search terms and compare them with the rankings you had when Google was showing 2000 back links. If your positions remain largely unchanged, there's nothing to worry about. If your rankings dropped significantly, there's indeed something wrong with your back links.