Ohh, ok that's good to know. I guess that's not a bug then.
But for the primary to secondary change I think there's still some confusion about what exactly is happening in my document after I do this.
Those bottom two colors should be the only colors in the document, but the Magenta plate has trapped what should be in the secondary. Adding unamed swatches does not return the Magenta colors into the swatches. If there is any way to trick the program into doing this I would consider that a perfect solution as then I could easily delete and replace that like you mentioned earlier. Let me know if anything is unclear.