Listing it as a "duplicate" is fine. The most important thing is making sure all collection agencies, attorneys and the original creditor is listed with addresses. It is wise to pull your credit report to insure the list is complete.
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You list both if you want both to stop contacting you or if you want to be able to make sure that these debts get completely removed from your credit report. You can list the second debt as either a duplicate or an additional notice party.
Most programs let you put down additional parties to notice. Put down everyone else who is trying to collect on the debt in that spot.
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Put down the entity that you must pay in order to satisfy the debt. It's possible the original creditor may still have some right to the debt but they usually sell all ownership and collection rights of a debt to a collection agency for pennies on the dollar; even if you try to pay the original creditor, they will refer you to the collection agency. Just mention on Schedule F who the original creditor was (for example, "debt transferred from XX"); if that is insufficient for whatever reason, you can easily amend the schedule later.
You can include the original creditor on the creditor matrix so they receive notice, at least. If they file a claim, then that is a good indication that you should amend Schedule F.