I apologize for overcomplicating things, and maybe it would be easier to ignore this. Or use the simpler solution at the bottom of the post.
But it's recently occurred to me that it would be a good idea to avoid ever doing writes to the entire capacity of a flash drive, including compactFlash. If you ever overwrite the whole drive, you could run into the same performance degradation problem that affects SSDs when TRIM isn't used. Therefore, I think writing a full drive clone back to a CF drive would be crippling to it's subsequent writing performance. Much of the data written back from the clone might be "empty" space, but the flash drive doesn't know that. From the standpoint of it's own wear leveling and garbage collection, it would behave and performs like it thinks it's full.
To avoid degrading a flash drive that doesn't have TRIM, the typical solution is to leave part of the capacity (around 20-25%) unpartitioned so that a chunk of logical addresses will never see a write. That way the drive will always believe itself to have enough unused space to continue performing properly during writes.
When you restore a clone, you'd only want to write to the boot sector and up through the active partition, but not perform any writes to the remaining unused space.
I'm not familiar with the tools mentioned here, but it might be best to use options for making an image of just the partition, so that it's easier to restore it the same way without needing to overwrite the entire drive. Boot sector is also needed though.
When I've cloned drives I've used the linux utility 'dd', but it's usage might be more cryptic than these tools are.
Or another solution, much simpler:
go ahead and make an image of the whole drive, but if you ever need to restore it, restore it on a new CF card that has larger capacity than the image. That way there will still be plenty of untouched addresses.
