I should update the advice above to say that I was referring to track-point positions used for bathymetric mapping - these are modified on import according to the specified transducer offset.
For Sidescan Mosaic, the transducer offset is picked up from the database and used when locating the sidescan image. So updating the workspace database will have an effect for sidescan, but will not have an effect on the location of individual track-points shown in the track and project windows.Because of this inconsistency, I would caution against simply updating the db but if you are only using the tracks for sidescan mosaic, then it may be acceptable as a quick fix. The right solution remains re-importing the tracks with the correct offsets applied everywhere.