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After the clone, the cloned partitions on the destination of course won't have the same drive letters as the source since the source partitions are already using those letters. Image Guardian won't be a problem since that's a file-level task and cloning is a partition/block-level task. Image Guardian won't prevent you from formatting a volume that contains Reflect backups protected by Image Guardian, for example, since that too is a volume task (though it requires admin privileges, whereas modifying Reflect backup files wouldn't necessarily.)
In terms of future backups to that disk, as long as you give the new drive the letter used by the old one and you're using Reflect's normal drive letter based destination targeting rather than unique volume identifier based targeting, yes you'll be fine.
In terms of using Rescue, if you were cloning your Windows disk, I would say that that suggestion can be worthwhile, especially if you have things like System Restore checkpoints you want to carry over. But since you're just dealing with a data disk, I personally would have no reservations whatsoever cloning within Windows, in fact I do it all the time. (If you're curious about the checkpoints thing I mentioned, when you clone within Windows, Reflect works from a VSS snapshot of the drive, since it can't work directly from the "live" drive on account of it being online and therefore subject to having its data changed during the clone. But Windows can and does exclude certain data from VSS snapshots, including System Restore points and the Windows Search index database, the latter of which can grow quite large and can be rebuilt automatically if missing anyway. By comparison, cloning in Rescue works directly from the disk rather than VSS since in that scenario, the disk can be taken offline to other access and therefore there's no need for a snapshot. But data disks typically don't have data that would be affected by VSS.)