In today's Daf, Rav Shmuel, according to Rashi, is not Choshesh (worried) about Peraon or Knunia because we assume that the borrower tore the parchment after paying the debt. BUT - if we are dealing with a Knunia, we can't be sure that the borrower actually tore the parchment, because after all - it is a Knunia, and it might be that the borrower is cooperating with the lender. Therefore, how can Rashi hold that there is no chashash for a knunia?
Nobody told us that there was a Kinunya. The Gemara is based on the fact that since a Shtar was lost, something is not right and therefore we have a right to be Choshesh. However, we will not be Chosesh for something that is unlikely. It is unlikely that a paid Shtar still be in existence, period. (It is of course impossible that the Kinunya was planned all along, for then why did they throw the Shtar out?)
D. Zupnik