。
I was worried about not having sent a reply.
Literal
Reply [object-を] sent-not [thing-こと] [object-を] was-worrying-about.
気にする means 'to worry about' or 'to be bothered by.' The nominalized clause 返事を出していないこと ('the fact of not having sent a reply') becomes the object of 気にする. The ~ていない marks the incomplete action, and ~ていました puts the worrying in the past.