If she was damaged in a way that changed her ability to lay or changed the way her pheromones are she will be superseded. Start checking for supersedure cells to see if they've begun the process. No supersedure cells, no problem.
I've done the same thing a few times. If your bees are hygenic they will clean her up in no time. Most of my bees are extremely hygenic and they usually remove the paint mark in a few months. I actually stopped marking my queens because of that reason, but decided to start back up again this year.
I did that once and it killed the queen (less than 24 hours). If I do it again, I will put the queen back in the hive before the paint dries. I have seen the bees clean wet paint off the back of a queen in about 20 seconds. You would have to recatch and remark her at a later date, but she would be alive.
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