Welcome!
Great to hear you watched the Rebuilding Your Feet Series and Pro Episode #3 The Flat Feet Solution.
Good to hear you CrossFit.

Wearing flat shoes makes your feet make the correction vs the shoe making the correction.
You’ll move to a lower profile shoe in stages. You are use to having alot of support so you’ll scale that back in stages.
There are exercises to strengthen your feet which can help build an arch. It takes some time.
Have you had exposure to these exercises?

When did your feet start bothering you?
Was it after beginning to implement some of the exercises from the episodes?
If so, it is from beginning to use parts of your foot which haven’t been used before or used as much before.

Are you wearing different shoes?
Any differences in your training? Increased volume or new aspects in training?