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were the original swatches spot color or process? If spot, you could try using Ink Manager to alias them to the new colors.
Yes, good idea.
The PDF ignores for the second color (cyan 50%) to make the change. Seems the problems from ID cannot be resolved in Acrobat.
I will manuallly change the colour in the tables: there are only 18.
The problem is that ID conserved a deleted colour, converting it to a new colour: Unnamed Color, as may be seen in the photo.