I didn't see any difference when encryption was on or off. My guess why is that the speed is due to link speed (mostly USB 2 or 3 speeds) and the HDD write speed limits.
By current definition a clone would not leave out files. A clone should be whole.
What you might be looking for is what Time Machine does already. That is, only the changes are copied over.
So you might be searching for another backup solution but since you have the cloner and Time Machine, you should be fine on backups right now.
I cloned my old Macbook Pro onto an external harddrive.
Then I bought a new Macbook, and set it up using the Time Machine backup of the old Macbook Pro.
If I clone the new Macbook onto the same external harddrive, will it be recognised as the old Macbook Pro, and thus only clone whatever additional files I added since the setup of the new Macbook?
The reason I'm asking is because the cloning of the old Macbook Pro took very long to encrypt. I want the cloning of the new Macbook to be recognised as an updated version of the clone of the old Macbook Pro so that it only clones whatever additional files were added/changed, thus taking a shorter time and without having to redo the entire clone and go through the encryption process again.
I'm using Carbon Copy Cloner, if that helps. Thanks!

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