Indeed, you will know that you copy is "not you". But what objective criteria could a third party use to make this distinction? If they are identical, how would your wife, for example, go about deciding which one you are married to? Is she married to both?
I just want to make something clear, though. I completely understand the "but it's not *me*" argument. I would, in all probability, not have myself scanned if it meant I would die. This sort of subjective bias is pretty hard-wired into our thinking. I just admit I cannot give an objective criteria to distinguish between the two.
Obviously, if the copy was perfect a third copy could not tell the two apart. If the copy was not perfect, they could be differentiated based on the imperfections: minute differences in the ratios of carbon isotopes?
The question is largely moot. The computing power necessary to describe the position of every molecule in a single bacterium at a given time does not exist, the technology to determine the position of every molecule in a single bacterium at a given time does not exist, with or without destroying the cell, and the technology to replicate the positions of individual molecules within a bacterium does not exist. Nor do I believe any of these is ever likely to exist, with the exception perhaps of the computing power necessary to store the information. For one bacterial cell. To store the information for a human body would require at least 100 trillion times as much storage just for the cellular information, not to mention the non-cellular components like bone and fibrous tissue.
According to wikipedia the average weight of a human cell is one nanogram. Let's assume it's all water. 18 grams of water has 6 x 1023 molecules and 1.8 x 1024 atoms. 1 nanogram thus has something like 1014 atoms. How many bytes necessary to describe the identity and position of an atom to the requisite precision? No idea. Still, we're talking about thousands of terrabytes (petabytes) or more of storage just to describe a single cell.
Feel free to correct my math. I may be off by a decimal place or two.