Hello Edgar
Thanks for writing to us with your health concern.
IBS is underlined by basic anxiety and depression which contribute greatly to the symptoms of IBS.
Pregnancy in itself is a condition of increased stress for women, due to hormonal effects, and hence many women undergo worsening of IBS symptoms during this phase.
As you rightly pointed out, most of the medications used to treat the condition are contraindicated due to adverse fetal effects.
I have gone through your reports.
The ultrasound scan is perfectly normal.
I would recommend an internal ( vaginal ) examination by an obstetrician as that would easily tell you if the pain is due to pregnancy related complications like an impending miscarriage.
In that case, the cervix ( mouth of the uterus ) would be shortened in length and would be dilated and loosened.
Since your wife does not have any spotting / bleeding and the pain is characteristically that associated with IBS, I suspect that it is indeed a flare up of IBS as opposed to pregnancy related event.
The mainstay of therapy for your wife is - to consult a good psychiatrist and undergo behavioural therapy, deep breathing exercises and relaxational techniques.
There is no scope for antidepressant and anti anxiety drugs during pregnancy.
Yoga / meditation / mild exercise will also benefit your wife.
The medications sound all fine.
Duphaston contains progesterone which will support the growing pregnancy , and Primolut Depo injections also contain progesterone in oil.
Some kind of progesterone is essential in your case to reduce risk of miscarriage as well as reduce any pain which might be due to subtle undetected uterine contractions.
There is no need of taking Primolut depo injection in my opinion, as you are already taking progesterone in duphaston.
Primolut Depo injections are based in oil and are extremely painful ( the injection site itself will cause pain and thrombosis and lump formation, risk of abscess etc ).
Hence your apprehension is justified, and you can go ahead and tell your treating doctor that progesterone has already been supplemented in your case via duphaston.
One word of caution, though.
Duphaston is banned in the US, UK and Canada - risk of fetal birth defects exist with its use in pregnancy.
The safest and most preferred progesterone preparation is vaginal natural micronized progesterone suppositories ( oral progesterone also causes side effects such as dizziness, nausea, drowsiness ).
Many excellent brands of natural micronized progesterone are available, such as Susten , Neogest, Microgest, Gestone etc.
Newer vaginal progesterone gels are also available ( Crinone gel, Susten gel ) which are easy to use vaginally and have excellent results with no side effects.
I hope this answer helped you
Please feel free to discuss the issue further with me anytime.
All the best with your pregnancy, Edgar and Namitha.
Take care.

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As a postscript, dietary modification is a big component of managing pregnancy and IBS both.
Eat small frequent meals instead of binge eating twice or thrice a day.
Take lots of liquids such as soups, juices, dal, buttermilk, coconut water, water etc.
Stick to fresh, non spicy, non greasy home made food.
Avoid eating outside.
Avoid gas forming foods like cabbage, broccoli, rajma , chana, leftover food kept in the refrigerator, beans etc.
Take lots of natural digestives like saunf , zeera, heeng etc in your food.
All the best.