On Bava Metzia 13a there is a discussion of a fear that the lost document might be a shtar k'na'ah, a document where one person is encumbers his property at one time even though he doesn't receive the money he is borrowing until later, if ever. What's the difference between a shtar k'na'ah, and a shtar amuna, which we know from the second chapter of ketubot is asur Also, why would a suspicion that the shtar may be k'na'ah prevent the beit din from returning it to the lender We learn in the second chapter of ketubot that even if both parties state that the shtar is not kosher, that it is a shtar amunah, the beit din will enforce the terms of the document
An Amanah is held by the Malveh. Here, we are talking about a Shtar held by the Loveh until the loan takes place.
The Gemara writes that if it is a Hakna'ah (which is clearly written in the Shtar) then we will give it back, except according to the opinion that holds Chaishinan l'Kinunya.