In case you experience timeouts while running a backup this page may help you. This sometimes happens when customers have either a large number of files or extremely large files. This is very easy to do but might take a few attempts to find the correct number. Changing this setting impacts the backup performance a bit so we want to try to find the highest number possible that will allow the backup to complete successfully.
In the settings section of WPBackItUp look for Batch Size then DB Tables Batch Size, the default value is 10,000. Please decrease the value by 1000 until you find the correct number that will allow you to do the backup completely and click Save.
If you need further assistance please get in touch with WPBackItUp Support and submit a ticket.