Sorry, I missed your earlier post.
The central section of the swath uses very few "pixels" to generate an image over a relatively large horizontal area. This is due to the way that slant-range correction works, and the fact that there is very little difference in the length of the direct route of the sonar beam vs horizontal distance when the angle of incidence to the bottom is high (approx 90 degrees directly underneath the boat). This gives reduced resolution, but not reduced accuracy as such. Conversely, areas further from the boat (horizontally) have an ever reducing angle which means that each "pixel" of the beam correlates more closely to the distance travelled along the sea floor, giving a higher effective resolution.
Although it may be beneficial to remove the lower resolution centre of the swath, increasing the water level offset to produce a gap in the middle of the swath is probably not the best way to do it. Instead, just use the upper range function to truncate the swath image and leave your gap, because otherwise you are adjusting the slant-range calculation for the entire image by changing the depth used underneath the boat.
The water-column offset feature is really supposed to be used as sparingly as possible, just to remove any last holes of water column that may appear e.g. to an incorrect depth reading or a local feature on the seabed. Ideally, offsets should be applied to as short a section of swath as possible - do this by cutting a track into segments in the Sonar Mosaic view.