Items in Zotero are global. They do not exist within a single collection. Instead, items are assigned to a collection and can be assigned to multiple collections. So merging two duplicate items into a single item is a global operation and will affect it in all collections. Also merging duplicates is not the same as removing items. Internally Zotero equates the item IDs for the two original items, which means that you do not lose any links between your reference library and documents containing those references.

It's not entirely clear to me on what kind of records you want to keep. Perhaps removing items from collections is more suitable for you (though that does not remove them from your library and they will continue to appear in "Duplicate Items" view)

This is a quick and dirty hack for automating the merger of duplicate zotero items.
In order to use this you will need to have your zotero library open in firefox and have a set of duplicate items selected in the duplicate pane.

Open a browser tab and enter: chrome://zotero/content/include.js


Then open the "Web Console" from the developer tools(there are other options like Execute JS too)


Then paste the following lines into the console:


var Zot_Dup_Pane = Components.classes["@mozilla.org/appshell/window-mediator;1"] .getService(Components.interfaces.nsIWindowMediator).getMostRecentWindow("navigator:browser").Zotero_Duplicates_Pane;


//note this will fail on duplicates that are not the same item type or it may crash if you have a large library - in which case I export subsections of the
//library and merge them in smaller sets - importing them into a new library at the end.
//You may want to change the while loop into a for loop with smaller iterations so you can control how many records are merged in each go

while (true){
Zot_Dup_Pane.merge()


}