I also have underactive thyroid (started out as overactive) and it's really very easy to treat and keep under control, compared to Crohn's and everything else most of us have. Yes, it's one more medication to take and one more thing to have checked a few times a year, but, in my opinion, it's nothing to stress over, compared to everything else we go through. If you end up having to have part of your thyroid removed, of course, that isn't any fun but, if it's like mine, you just take something once a day and occasionally have it checked. I have noticed that changing Crohn's medications can throw off the thyroid levels so, anytime you make a major medication change, you may want to have your thyroid checked again. We just had to decrease my Synthroid due to changing from Remicade to Cimzia. So, don't let this stress you too much. Hope you get everything else worked out quickly and don't have any problems in the meantime.
...rejoice in our sufferings, because we know that suffering produces perseverence; perseverence, character; and character, hope. Romans 5:3-4