You may be able to GENTLY sand down the thick places with a fine sand paper and a light
hand. Wear a mask, it could be lead based paint! Then color match the existing ensolite and paint with a pouncing motion to further duplicate the texture of the existing ensolite.
I would not like the thought of leaving that mildew under there either, but Kilz or Bulls-eye primer will keep the mildew from coming through if you must cover rather than "rid".
I use a mixture of 1:1 acetone and xylene to strip paint from fiberglass but it would probably goo up the ensolite finish. You could try testing various strippers in inconspicuous places (like in the closet or under the sink) - just depends on how much there is to do and how ambitious you are feeling. Hope you get it resolved to your satisfaction.