I have the same problem since version 3.0 (I'm using version 3.3.0.1 right now). It seems like incremental and full backups does the same. All the artifacts of the included repositories are copied to the backup folder instead of only the new ones. So, some time ago, I've created an issue related to this (https://www.jfrog.com/jira/plugins/servlet/mobile#issue/RTFACT-6409) but still there are no activity.
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