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Homeopathy cannot harm our bodies. But if you have doubt then no remedy for doubt. For acidity and flatulence, you can give her the below tablets-
Asafoetida tablets three or six, thrice in the morning, noon or evening, and at night.
Lycopodium 30 tablets five pills in the morning and evening.
Carbo veg 30, five pills in noon and night.
Once her digestion will improve she will be fine soon. Start above mentioned medicines. Allopathic medicines will not give relief in the long term. Alfalfa mother tincture will help with digestion improvement with recovery from weakness and all. Continue with these medicines.
Stop Arsenic alb.
Give a follow-up after 15 days, and if any changes then in between you can give a follow-up.