Baby constipated😭

My baby was suffering bad with gas and reflux, so our doctor advised us to switch to soy formula. We did and it was amazing! No more gas or reflux. Well it was for a week, and then he got constipated. Tiny pebbles of poop and straining SO bad while he’s going. He’s 11 weeks old. In the morning he will stain and it’ll be hard, then he’ll poop like normal in the afternoon again. But he’s in so much pain while going in the morning. He still goes daily at the same time twice a day. He’s on probiotics too and has been for 3 weeks. It’s been almost 2 weeks of soy now. Should I call the doctor? I did switch back to total comfort for 2 days and he spit up horribly and had bad reflux again. So the soy helps a ton, just not with pooping lol.