I am having terrible difficulty on Daf "12" Omed "2" in understanding the gemorah on the mishna - Motzie Shtar Chov.
I don't know exactly what is troubling you so I'll give you the general ideas and please feel free to write back any specific questions.
A Shtar is different than other lost articles, for it can have only one of two owners, either the Malve or the Loveh. In addition, the ownership of the Shtar has ramifications larger than the document itself; if it belongs to the Malveh it means that the loan is unpaid, if it belongs to the Loveh it means that the loan is paid.
Returning it to the Loveh is tantamount to destroying the Shtar. As for returning it to the Malveh, there is seemingly only one reason not to return it, that maybe it is paid. Therefore, if the Loveh admits that he still owes there should seemingly be no reason not to return it to the Malveh. However, the Mishnah writes that if there is Shi'abud written in the Shtar, and therefore one can collect from sold properties, than the Shtar relates to others as well as the Malveh and the Loveh. Since the Shtar is suspect, for in general one does not lose a Shtar we are afraid that it is not genuine; that it was predated, and if we return it the Malveh will be able to collect from properties whose sale predated the loan. Although we do not question every Shtar which comes before us, this Shtar is worse for since it was lost it is suspect.