I am in an after effects template that I bought. I am in the project section, I click on one of the comps and then control-D to duplicate the comp... then I toggle in the projects folder between the two and can see that they ARE NOT DUPLICATES! They aren't the same...similar yes, but not he same. Why? How do I ACTUALLY duplicate it with all of its properties?
Without knowing any of the specifics of your project, nobody can tell you anything. From the sound of it, the project simply uses shared nested comps and as you keep modifying those, the divergence across comps becomes more obvious. Just duplicating a comp does not automatically duplicate its associated sub-comps! Other than that there could be other things like camera views being different or random seeds of effects and expressions having changed, resulting in a different look, which would also be normal a lot of time.
If you duplicate a composition in the project panel you get a duplicate. Open the original in the timeline and open the duplicate in the timeline and check that the CTI (current time indicator) is the same and both comps are being viewed by the active camera and they will be identical.
The only thing that will foul something like this up is an expression in another comp that is looking for comp name that it cannot find. Without understanding the complete structure of your template it's impossible to say that this may be the case.