Non-disruptive and efficient migration of data across cloud providers

Data containers are stored at a first cloud and include file segments managed by a deduplication file system. Metadata containers are written to a log, identified by a container ID generated sequentially, and include references to data containers. An index is maintained to map segment fingerprints to container IDs. Upon starting a migration to a second cloud, a checkpoint is created identifying a container ID at a head of the log. During migration, the index is updated to map fingerprints of migrated segments to new container IDs, and referencing new data containers having the migrated segments and written to the second cloud. A request to read a file is received. The index is examined to identify a container ID associated with a data container storing segments of the file. Based on the identified container ID and the checkpoint, the data container is accessed from the first or second cloud.