You don't need the filter if flash is the main light source because, with the exception of a few specialist infrared flash guns, the output from the flash should have the same colour balance as daylight.
If the flash is being used as a fill-in light source then you would use the FL-D filter to balance the predominant light source (flourescent), however, there may be some colour cast.
Because flourescent light sources are discontinuous, that is they do not emit a full range of light across the visible colour spectrum, even daylight type flourescent lights cannot emit across the full spectrum. A FL-D filter can not produce a perfect correction of colour balance from fluorescent to daylight but it will improve results considerably.
Due to the problems with colour correction flourescent sources are not usually recommended for colour portraiture.