Had a root canal recently and the endodontist told me I have a fistula in my upper palate leading from the area where the tooth in question was infected. After the root canal it was expected to heal (close) and "we" waited several weeks for it to do so. It didn't. Am on antibiotics even though the dentist says the fistula is no longer draining and there is no sign of infection. I have asked both of my dentists if the presence of this fistula could be related to my history of IBD (ulcerative colitis). Both said, "No." I'm curious if this is an extra-intestinal occurrence. I need to have the closing step of the root canal but can't because of the fistula. My fear is it won't heal (close) and the tooth will have to be extracted! Anyone have this experience?
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"No" was probably too strong a response on their part, though it sure might be unrelated to IBD. If you have Crohn's now (rather than UC), any part of the GI tract, including the mouth, can be affected, and fistulae can develop in the mouth. Good luck - I hope it heals up soon.
I suppose anything is possible, but I've never heard of a tooth root being part of the GI mucosa. I think this is more in line with "stuff happens." Even in the general population this sort of thing happens. With the abscess going that far, it may be too far gone. Hope that's not the case.
Jan 
A dental sinus should resolve following a successful root treatment. I don't think it is likely to be in any way linked to GI disease as it is infective not inflammatory in origin. Root canal treatment is not always successful though there are still options if it has not worked. A re-root treatment may be all that is required (it may simply be that a canal was missed first time round - upper molars often have an extra canal (the MB2) though to improve success rates a re-treatment may be better carried out by endodontic specialist using a microscope as these canals can be very difficult to locate sometimes). If this still fails or is not an option an apicectomy may work though before embarking down this root have an informed chat with your dentist about the implications should you subsequently want implants as this can result in less/poorer quality bone in the area.
Are you sure the root treatment has been completed and not just an inter appointment dressing? Feel free to message me any queries (I'm a dentist).