Best advice here is to decrypt the encrypted partition first. Software like HDclone don't always do a sector-by-sector copy, and if they don't do that then you're stuffed with the encryption.
(of course, if your encrypted volume is a container file then that should still work fine).
Sounds very risky to me however, as your eggs are out of the basket while you build a new basket. Or to put it another way, clone it to another HD, borrow a USB from a friend, backup anything you don't want to lose before etc etc..