I ran a waterbox with a broken baffle for years and never had a single problem. I did cut it open a while back, but I probably didn't need to. The centre pipe that connects the two chambers comes loose and clunks around, but that about it.
When you cut it open (if you can be bothered) make sure you cut down the side of the plate that runs through the middle, otherwise it will take you a long time, and have to get a new plate put in as well!! Thats not likely to happen anyway. When you have it all apart, clean the hell out of it and also clean 1/2" around the are to be welded (both baffle and box itself) with a polyfan/flapwheel. Doing this will make it easier for the boilermaker to weld, and will cost you less and you are doing all the prep.