The Phal's pot has been stuffed by the store with mosse and I can see that some of the top roots are rotting. Can I repot it eventhoug it is flowering?
Well, I heard you're not supposed to. Mine were stuffed they way yours are.
I re potted them in sphagnum moss and one by one, the flowers just came off. Now I have two separate 'chids with not a single bulb. They look like two sticks sticking out of the pot. I'm actually going to try to get help for them right now. Personally, I wouldnt recommend repotting.
I think as long as you handle the plant with TLC when you transfer it & try to disturb the roots as little as possible it shouldn't be a problem. I bought an oncidium sweet sugar a week ago in full bloom & I actually removed a psuedo bulb & got two plants and there hasn't been any signs of trauma to the main plant.
However I have read that some species like a crowded environment, so hopefully someone with more knowledge will advise you.
Generally, it's not a good idea to transplant a plant in bloom, but if the potting medium is so bad that you're risking losing the whole plant if you don't, go for it!