The OS does not get confused once it is up and running. I had some fun times initially where I could not figure out which bootloader was loading which install. It was actually the hard disk based original bootloader that was being used even if the OS loaded from M2 SSD. After figuring this out, I changed the UUID using some Linux tool. Now there is no confusion.
To avoid this in future, I want to keep the partitions UUID intact, while only reflecting the contents. This is probably not possible with free versions of Macrium etc.