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I'm using a Mac and it doesn't act the way you describe.

  #1,  If I have one of the layers highlighted and other layers linked and push just the trash button without any other button being pushed I get the message (Delete Layer #x ) what ever that number the highlighted layer happens to be.

#2   If I repeat the above process and this time hold down the Option button it deletes the  layer right away, without any message.

#3   If I repeat the process again this time holding down  the Control button I get the same thing happening as I  did in the first example.

Off the topic slightly , if I have a number of layers linked and then highlight another layer does that layer then also become linked  ?

Thanks for being so patient