Once you have backed up your vault store partitions, the Storage service marks the relevant files as backed up, and this removes the entries from the WatchFile table. The storage service performs these tasks at preconfigured intervals. You should wait for the WatchFile table to reduce in size before you proceed with the upgrade. If you do not wait, the Storage service can take some time to restart after the upgrade is complete. You can use the usage report at http://evserver/enterprisevault/usage.asp to check the number of files in the Awaiting Backup column.