Ubisoft recently released the 1.1 patch to include several new bits of free content and including some new issues.
The 3.9 GB patch that included the new Incursions content has also led to the “deletion” of some players’ characters. Ubisoft is already on the problem and has released a statement.
To sum up, Ubisoft explains that a server that wasn't synching correctly apparently caused the problem. It corrupted player data, making it unreadable by the system, so it assumed there was no character. With approximately three hours of server downtime, Ubisoft says that it can recover those lost characters from April 12 at 3 AM EST. If you made progress from that point onward, it will unfortunately have been lost.
The issue seems to have run across several platforms. CG Magazine has reached out for confirmation on which ones specifically. You can contact Ubisoft support if you’ve lost your character and read their full statement here.