Hi ginger,
Well since PD advised you to change, just give it a change and monitor the situation. Who knows your gal's skin will improve.
Every babies will have some degree of phlegm, it's a matter of more or less amount at that time. There was a couple of times my boy threw out his milk, together with some of the phlegm too. Now, his phlegm is still with him, well this is something we as parents can't do anything about it.
I may not agree that it's entirely due to FM that your gal's got the phlegm. Every baby is specially in their unique way. Their bodies may belong to the heaty category or the more heaty category too. May I know how old is your darling? So long your gal poos well, that shouldn't be a problem. If you have doubt, feel free to call your PD for further advises.