The issue, which was caused by the most recent 1.1 update, had made some Xbox One gamers’ characters completely unplayable.
Ubisoft has promised users their characters are not gone and all the missing data will be restored as soon as possible.
The publisher told the BBC: “The issue was caused by a malfunctioning server that couldn't synchronise character data correctly and corrupted them instead.
"The game client was unable to read this corrupted data, and simply assumed that the character didn't exist.
"Once this has been identified, we were able to restore the server to its normal functions, thus ensuring that the issue will no longer occur for other players.
"For those who experienced the issue, your character is not gone. We are currently working on a fix that should make it available shortly.
"Implementing this fix will require a server downtime, and we will let you know when we are ready to perform it."
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The best-selling Ubisoft game has earned mixed acclaim since its launch in March.
High hopes were replaced by decent reviews, while a myriad of issues affected early adopters.