In Venezuela, when they had fun race competitions, during stages where you had to cross a river and the vehicle practically sank, if water got into the engine, they would do two or even three oil changes to get the water out. I think, and based on what kikemec said, that two transmission oil changes should be enough. For the first change, wait 10 minutes with the engine running, obviously shifting through all the positions of the gear selector to allow the water to drain from the transmission valve body. Then proceed with the second oil change and test the transmission. Remember to drain the oil from the torque converter with each oil change. If your transmission doesn't have a drain plug, take advantage of the opportunity and install one. I did one on mine, which is a 4L30E, and it really makes the job easier by draining the oil beforehand instead of waiting for it to soak you. Let me know how it goes. Best of luck!