What kind of data is on the HDD ? ?
Are you saying that Aceonis does not rcognise both externals ? ?
If not you can hool up only the HDD you want cloned and have Acronis create and save the image to your internal for now...then power down...unhook that external...and hook up the blank external...power up and clone away.
NOTE: I highly suggest verifying the image before cloning...takes a bit longer buy well worth it.
It's under the Tools section in Acronis.