6 month old with IBD symptoms

Hi everyone.
I stumbled across this forum while looking for answers about my 6 month old's symptoms and potential diagnosis. Just looking for a bit of insight if anyone has had a young child diagnosed with IBD. Here's a quick rundown of her story-
From 2 weeks old she had mucus and blood in her poo, every poo. And pretty much had diahorrea everyday. She was exclusively breastfed, so we put it down to a milk protein intolerance, as her older brother was diagnosed with it.
So after cutting out dairy, soy and gradually other allergens as well, with no change in her poo and a slight weight gain drop, we moved onto Elecare formula 10 weeks old. She developed reflux with blood in it so was put on Nexium.
We got referred to a great gastroenterologist, and she had a endoscopy and colonoscopy at 4 months old as she was also starting to drinking less formula. The initial look seemed ok, and most of the biopsies came back fine, apart from one in her left colon that showed Paneth cell metaplasia. The gastroenterologist was puzzled by this as none of the other biopsies came back with anything suspicious, so we are treating her with Flagyl for 4 weeks. A few days ago she did her first normal poo ever! I couldn't believe it! And she has started drinking more milk again.

So she hasn't had an official diagnosis yet, but I'm thinking if the Flagyl has had that much affect, then there must have been something going on in her gut that needed treating. Plus everything I've read about Paneth Cell metaplasia in the left colon points to IBD.

Has anyone had the Paneth cells come back on a biopsy, or been diagnosed at a young age?

Many thanks :)

Thank you for your quick reply :)
She's had numerous stool samples and none have come back with any bacteria or parasites etc. I did have antibiotics intravenously during labour as I tested positive for strep B a couple of weeks prior, so maybe that affected her somehow? I'll start the probiotics this week, I didn't want them to mask any effect the Flagyl was going to have. Yes it's a bit scary to have her on them for a month too! I'll do some research on MAP, thanks for the suggestion.

The gastroenterologist wanted to try a sulphur medication (I can't remember the name of it!) but he decided it was too risky on a little one.

I read that article too, there's not much info on Paneth cells out there, which our doctor told me too. He said it could be the start of something brewing, or it could be nothing. Hoping for the nothing!
There was a bit of inflammation on the valve between the bowels, but not enough to explain the amount of mucus and blood that she was producing.

Our doctor thought it could be something going on in the intestines too, as obviously you can't see up that far with a scope. Occasionally she would have a horrible day with no poo, but lots of straining and being grumpy, and then would produce a huge mucus poo, kinda like its blocking her up and causing an obstruction. She'd be so happy once it had passed.

I had a quick look at MAP infections, really interesting stuff, I'm all new to this so slowly learning all the terms and meanings :)