In the Metadata API, individual versions of a file are represented by a ContentVersion object record. You may have noticed that there are fewer ContentVersion records being backed up than files in your org.

This is because users with View All Data permission can only query files they have access to — including files in their personal library and in libraries they're a member of, files shared directly with them, files posted on their profile, and files posted on groups they can see. 

In order to be able to query all files, including files in non-member libraries and files in unlisted groups, you need to enable Query All Files permission (release note) for your backup user. This permission is disabled by default in Salesforce.

To enable the Query All Files permission, you'll need to modify an existing Permission Set  or create a new one and assign it to your backup user.