The present invention relates to a system and method for improving data deduplication for eventual consistent for distributed storage systems. Eventual consistency poses significant challenges for deduplication systems. This is because data storage is often spread over many different notes and up-to-date data may not always be available. A significant component of deduplication is creating pointers to older copies of identical data and deleting the later copy. In a basic implementation, this creates an eventually consistent vulnerability. If an older copy of the pointers to the data is retrieved (in the form of a metadata file), it may be pointing to a copy of the data that is no longer available. The present system and method solves the problem with eventual consistency vulnerabilities by introducing a level of indirection and creating manifest files for each file (vessel).