Evolving something with a Paint counter is supposed to remove the counter. It does not on tcgone however.
The only information I have to gauge is WotC rulings from 2001
Q. When can you remove the coloring counter from Smeargle? Does the Coloring counter remain on the defending Pokemon if it retreats, evolves, etc. (like “Char” counters)?
A. The coloring counter actually isn’t on Smeargle, but the only way to remove it from the Pokemon it is attached to is to evolve it or have it leave play. Just like Char counters, benching does not remove it. (Mar 22, 2001 WotC Chat, Q13 & Q40)
Q. Will Full Heal get rid of the Paint counter, or is there another card to do that?
A. No. You’ll have to evolve or scoop up to get rid of it. (Mar 22, 2001 WotC Chat, Q113)