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Send in the clones!
Some software, as an anti-piracy measure, will notice that the drive has been replaced, and will require re-activation or re-registration. If you have the activation or registration code, simply enter it when prompted. If not, a call to the vendor, with an explanation of the cloning mechanism that has been done, will allow them to provide you with a new activation code.
If you want to give it a try, I recommend Partition Magic from Symantec or True Image from Acronis.