If you want to make an order from external source, but the external record has duplicates in your catalog, Koha now uses the existing record instead. Unfortunately, the user is not made aware of this fact.

IMHO Koha should warn the user and offer three choices: 1) take the existing record and order [current behavior], 2) use the new duplicate record and order [for some reason..], 3) go back to the basket without ordering [I already have the book!]

Check this behavior in current master by:
1) Choose a record in your catalog, possibly coming from an external Z3950 source. Otherwise add a record from an external source (Z3950 search).
2) Go to Acquisition, add new basket, add new order from external source. Select the same title (make sure it is really a duplicate: title, author, isbn, itemtype).
3) Save the order (add quantity).
4) Check the new line in your basket. Does it point to your old biblio? If so, you had a duplicate. But Koha did not tell you! 

Test new behavior of proposed patch:
1) Install patch. Repeat step 2 (add order from external source).
2) A new form should come up now. See screen shot. Offering you the three choices mentioned.
3) Test each one of these choices and check the biblio number of new order lines (hovering your mouse above the title of the order line).