Like woodsy stated above, not an issue.
Cerakote should not be painted over fully cured Cerakote (doesn't bond properly). If your barrel is already cured with cerakote, it will need an acetone bath, get blasted, gassed out, and repainted. Same process with a non-cerakoted barrel, but the first coat is one color for the entire barrel, then the flash cure, then the stencil and second color applied, then another full cure bake (bonds all the colors together, very strong).
It is possible to vinyl cut a high heat stencil and tape off just the area you want painted if you want to leave the barrel with whatever finish it may already have. But this would be less durable in theory. I have painted just the flute cuts in a stainless barrel once, no issues there so far. Just gotta run the steps a little out of order. Soak the part, gas it out, tape it off with media resistant material, blast it, wipe it down again, spray and bake.
I have also accidentally fully cured a part I needed to 2 tone. Instead of starting completely over, I wiped the cured cerakote part with acetone to get it clean, taped it off, blasted just the section that needed painting aanother color, re-painted and cured it again. Blasting being key to getting the part ready to accept the coating. Otherwise a new coating will not adhere to a fully cured coating. So far I cannot tell a difference in wear. But, that was for one of my own rifle, I wouldn't cut corners like that if I were to paint a part for someone else. I would blast it all off and start again.
Cerakote isn't difficult to paint, but to do it properly is time consuming, and requires vigilant prep work. Time is money if you are hiring the job out.