Q. Do I really have to worry about duplicate RefWorks records if the two members of the duplicate pair are in different folders?
Write-n-Cite, the program used to insert citations from your RefWorks database, doesn't provide a way to limit citation insertion to references from a single folder. If you happen to insert citations based on both members of a duplicate pair into a Word document, you will encounter problems. The reference will be listed twice in your bibliography, and, if you are using a numbered in-text citation style like the NEJM or AMA style, the in-text citations created using the different members of the duplicate RefWorks record pair will get different reference numbers.
Because of these potential problems, it's best to check for duplicate records every time you bring a new set of references into RefWorks-- do this immediately after importing the references.
If you organize your references in folders, I would recommend turning off the RefWorks' automatic duplicate marking feature to make the duplicate deletion process easier. To turn off the automatic duplicate marking, use the RefWorks "Tools" menu to select "Customize", mark "No" next to "Automatically mark duplicates" and then click on the "Save" button at the bottom of the page. There are many reasons to turn off the automatic marking. One of these is that both members of a duplicate pair or the wrong members of a duplicate pair (the older members) are sometimes marked for deletion. Also putting references you wish to keep into additional folders before deleting the newer pair members is made much more difficult by automatic duplicate marking.
To check for duplicates, as you probably know, you use the RefWorks "View" menu to select "Duplicates" and then either "exact match" or "close match". Check the duplicate pairs that are lined up by RefWorks to make sure they are really duplicates. Drag the reference that you're keeping into the folder previously occupied by the member of the pair that's destined for deletion. The single record will now contain labels that indicate that it belongs in both folders (it isn't duplicated it just gets two (or more) folder labels).