How to move references from one folder to another within the same library

I have several folders and sub-folders within a single library. Because there is no way to mark an article as being read, I've set it up so all of my unread PDFs are in one folder. As I read them I want to move them to one of the folders that has the category labeled. I also sometimes have to move PDFs to different folders depending on how I want that PDF framed within my research.

When I do this, the PDF is now in the category folder, but a copy is also still in the "unread" folder. When I delete it from the "unread" folder it then also gets deleted in the category folder. How do I move a PDF (not copy) from one folder to another within the same folder so that it's not in 2 places at once?
  • Zotero does not have folders, but it has collections. Collections do not work like filesystem folders. A Zotero item can belong in multiple collections. Reading this should help: https://www.zotero.org/support/collections_and_tags

    For marking an item as "Read", you should probably use tags, rather than copying (drag) or moving (shift+drag) items between collections. Just create a colored "Read" tag and drop your item over it (you can also use number shortcuts for that). Quick and simple. I think the developers have a plan to have a "Read" tag implemented by default.

    Removing an item from a collection does not remove it from another, unless you actually deleted the item: Those are two different actions, and show up as "Remove Item from Collection" vs "Move Item to Trash" in the context menu (right-click on an item).

    It is also possible that you checked "Show Items from Subcollections" under the View menu. That means a collection will display items that are not necessarily in it, but are present in one of its subcollections. If that option is checked, removing an item in a subcollection will make it disappear from a parent collection, even though the item was never in the parent collection.
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