Here's why. Windows may not like changes to the boot drive like this. It has some odd (not really) idea about the boot drive location/connections.

Be sure to test after the clone.

In parting, I do something similar but use CLONEZILLA to write an image file to my external HDD. This way I can write more than one backup copy out. To restore I install a new blank drive and use CLONEZILLA to copy in the image file.
Bob