I've taken amoxicillin a couple of times for sinus infections.
I did have an increase in D while on it, but it wasn't too bad, and I returned to normal a few days after finishing the antibiotic.
Of course, everybody is different, so you may have better or worse effects. It's just about impossible to predict how an individual will respond to it.
I would take probiotics and/or yogurt while on the amoxicillin.
If you're undergoing Crohn's tests, definitely be sure to let your doctor know.