Yes, normally they can tell that the license is exchanged because there is a mention at the back, on the bottom part, (at the very least, for the new, credit-card format licenses) with a code indicating the country that originally issued the license. It looks a bit like this on my exchaned French license (my own picture, I deleted out some details, but I left the part with the country code):
(B) 70.0123456789.XX (XX being the country code)
Another example (Reverse of Portuguese driver’s licence showing the number of the previous non EU license):
So I believe that either Column 12 or Row B on the back is the place on your license that mentions whether your license was exchanged and which country originally issued it.
Check out this post that shows an example of someone who tried this (US license -> German license -> French license): Ohio>Arizona>Germany>France driver's license conversion?
And my own EU driver's license that was exchanged from a non-EU country.