When the Nuxeo documents that reference a blob are deleted, the blob is not deleted (for important efficiency and backup consistency reasons).
Since Nuxeo 5.4.2, there is a "garbage collection" button available into the Admin Center/System Information/Repository binaries section.
Since Nuxeo 5.2, using VCS as backend, the content of files (blobs) are stored on file system in the $NUXEO_DATA_DIR/binaries directory (depending on Nuxeo version and server type, it will be $JBOSS/server/default/data/NXRuntime/binaries, $TOMCAT/nxserver/binaries, or $TOMCAT/data/binaries).
To delete these blobs, before Nuxeo 5.4.2, you need to run the following script:
Starting with Nuxeo 5.3, this script is also available in the $NUXEO_HOME/bin directory.
For safety, you should back up your data directory before starting this procedure.
From the documentation of the script: