Enterprise Vault backup mode is a kind of read-only mode:
to make sure that the data in the SQL databases and the data stored on the partitions and index locations is consistent.
Backup mode blocks any modifications to the archive and SQL. End users are able to delete shortcuts and perform a manual archive. But in reality, the archive and restore actions aren't commited. During the period that EV is in backup mode, such user actions will accumulate in the private queues of MSMQ and if you run checks on the EV site, it will complain about unsaved savesets.