Yes, soy along with Calcium and Iron effect the absorbtion of synthroid meds.
The first time I was on IP and was at my heaviest, I was careful and wanted to make super sure that my synthroid was going to be absorbed so I moved my thyroid medication to the pm, just before bed since that would be the time farthest away from any soy/vitamin product I had taken thoughout the day.
I lost about 30 lbs on IP and my TSH did drop a little but not much. I was happy that he kept me at my same dosage
Now that I am near goal, I take my synthroid alone in the am then vits at noon with lunch, and calcium etc with dinner and more calcium before bed. I have no problem with this. I get my levels monitored often because I had thyroid cancer and they are always about the same with this routine.