I had this problem as well. They never seemed to fade that quickly though.
What I do now is I airbrush them an hour of so before I use them. I keep flowers ready like roses or leaves or calla lillies any kind really. Then whenever I need some I just load my sprayer with color and spray them all down.
My ribbons and flowers faded overnight when I used the Wilton colors. So I tried Americolor and this powdered color (I think its' called Candy Kake or Kake Candy food coloring powder) and both of them really hold the colors well in gumpaste and fondant.
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