Mate, you oughta sent it to the bin, now I had to bin the other one

If you modded flood out of the game and there are still provinces with flooding, it means that you didn't start a new game and your modded changes won't take effect until your next new game (provided you also remembered to deleted your rwm file after modding, which you must for changes to take effect at all).

So to remove flooding penalties from a previously flooded region, it must be hit by yet another disaster. Sad but true.