Flat roof leak

Found water coming through the light fitting in our bedroom last night, so the flat roof above will need re-felting, that I guess is inevitable however I seem to remember when the extension was built that the builder half filled the gap between the beams with insulation, like he rolled out the insulation from underneath put it between the beams and then held it in position with some lats half way up the beam, the question is does the space need an air gap or should I take this opportunity to strip off the roof completely install a load of insulation between the beams and then re do the roof ?
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