You will most likely need to get your fingerprints done again for your N400 application.
I asked the officer when they were taking my fingerprints for my replacement green card if USCIS would be able to use these fingerprints for my N400 application and he stated that it is NOT possible since each application go to different areas.
In short, each application is considered a separate thing.
BTW, this was definately within the 15 month timeframe of fingerprints being valid. This was in the San Jose CA DO so it might be different.
Hope this clarifies things.