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We would like to create two plates with the same pantone but already defined in the pdf.

is it possible from pitstop to duplicate a colour channel and leave it with a custom name?

Or maybe create a new layer with this pantone?

Any idea

You can use the copy/paste actions:
Select spot color (now one or more objects are selected)
Copy
Select all (this is necessary because pasting is done on the page level, not on one more objects)
Paste (make sure not to move it)
Select last added objects
Change color
Add objects to layer with name (this is optional)

Thank,s @freddyp

could I change the name of that duplicate pantone to a custom name?

Open the Color Picker in PitStop; you can do that via the PitStop Color tools or via the Actions in the Inspector in the Fill window. There you can create a new color in the Local group and you can name it the way you want. Make sure to check the box "Define as Spot Color alternate values" so it creates a spot color and not just a CMYK/RGB/Gray/Lab color. Once defined you can use that color in the "Change color" action.

Fantastic