Always keep photcopies
Sankrityayan and gc_from_oh do not worry, there are so many of us got a second FP from NSC. We got second FP as early as Dec 2002. We called FBI, NSC and local INS office to get it resolved. Call NSC and find out, once your FP are in their database, then you do not need to worry. Also, if the 2nd FP notice was generated by NSC, then your attorney would also recieve a copy. If 2nd FP was generated by FBI, for not having a clear FP first time, then only you would recieve the notice, this notice does not look the same as a recipt notice from INS/BCIS.
With my experience with various Govt Agencies in the world:
Keep Photocopies of documents that you submit or present in front of a govt officials, or even if you are mailing the original docs, so as to avoid a situation as not having a reciept in hand.
A friend of mine had sent his passports to St Louis for visa stamping. His passport got caught in Anthrax examination lot. He had to live for more than 8 months without a passport, H1 doc and copies of the same.