soy based formula help 😣

Hey ladies. My baby was taking enfamil gentlease cuz she was very gassy on enfamil premium. I had the same problem with my son and gentlease worked wonders. Anyway, when I switched her to gentlease I was also breastfeeding. She was pooping sooooo much like 9 out of 10 diapers were poop each day. I thought it was the breast milk so I stopped nursing and just pumped and stored for about 3 days. The poop didn't stop.  By this time it was time for her to see her pediatrician. I told the doctor about this and she recommended we switch to a soy based formula. I got a can of prosobee and it seems to be working. Today I went to the store and the were out of prosobee so I got isomil. Would it mess with her too much to switch between enfamil and similar?? I also read that soy based formulas are bad for babies. Does anybody have any experience with this?? Please help!!! 😔