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Is this new hard drive a new destination drive or a new source drive? Changing destination hard drives shouldn't cause duplicate job occurrences, in fact for some users, rotating the destination disk at regular intervals is part of their strategy, and their schedules work as expected because the scheduled task itself doesn't care or even know what the destination is; the task just says "Launch Reflect and have it run this job file".
But are you determining that duplicate backups are running based on seeing two job logs under the Log tab when your schedule should only be causing one, or are you just looking at the Date Modified timestamp of your backups? If you are in fact seeing two job logs, check the Scheduled Backups tab in Reflect (all the way over on the right) and see if there are any redundant schedules there. If on the other hand you're only looking at timestamps, there are reasons that Date Modified timestamps of existing Full or Incremental backups can be updated when a new backup runs, but that doesn't mean a second entire backup job ran. Based on the fact that you only see a few minutes difference between these backups, it sounds like what may be happening is that when a new Incremental backup runs, it's performing a consolidation operation to keep your total number of Incrementals within your retention policy settings, and when a consolidation occurs, it will change the Date Modified timestamp of at least one backup in your set, and possibly nearly all or even all of them, depending on your retention policy settings and whether you're using Delta Incremental Indexes. If you haven't already, go to the Log tab and look at the log for the most recent job that ran for this definition file to see if you see any mention of consolidation occurring.