Hi! I'm coming to this thread a bit late, but I wanted to comment. I'm a birth doula, and I have a particular interest in Reiki and pregnancy/labor/birth.
I received my Master's attunement when I was pregnant with my second child, so she also recieved a Master attunement. I did Reiki quite a bit while I was pregnant.
Rather than skip the stomach, I found that I was led to focus there more extensively. The positions were held longer, and as my belly expanded, I had up to 5 hand positions for the stomach (three horizontally - as with the torso, both hands on the sides, and hands above and below - cradling). As the baby is growing so much, extra energy can only be beneficial. I know we're supposed to 'ask permission', but Reiki does not violate free will. If the baby doesn't want it, Reiki will not effect the baby. Period. But it would help the mother, if she is open to it.
I would also highly suggest that you send Reiki ahead to her labor. Every now and then when the thought came to me, I would send Reiki ahead to myself for the labor, because I knew I would not be able to concentrate on it then. I even sent it ahead to my midwife. I also found it helpful to send ahead to doctors appointments, especially if testing or internal exams were necessary. It helped me to relax and stay focused on the info I would be receiving.
Congratulations and best of luck to her!