I believe there are some labour laws regarding absence due to recognised illnesses.
Have you spoken with human resources about this, sometimes they can help.
There will be others on this forum in a better position to help you and I am sure someone will be along soon.
Being in Canada our rules may differ.
It must be very upsetting for you, not only having crohn's but also threatened with job loss because of it.
Wish I could be more helpful
Feel better soon
Hugs and best wishes
Trysha