I would say just when you re apply to write an explanation letter for your current situation exactly because they approved your application, it means that they have created a file with a number for you and entered all of your information on their database. Furthermore, there is a question on (schedual 1 background declaration) of the application forms asks whether you have ever applied to any kind of visa for canada and you must answer yes, as a results, you will have to write explanation for your answer at the space provided for that regard.
Just mention that it was mistake because they are very close to each other and you don't have enough knowledge about NOCs system, and describe the situation exactly as you stated above, I am sure that they will consider the good intention in your case.
Have a look at this :
"Visa officers may also check previous applications to corroborate any information provided in the FSW application. Applications more than 12 months old, however, will not include the most recent information about work experience."
The source : http://www.cic.gc.ca/english/resources/manuals/bulletins/2009/ob120.asp
Good luck.