Hi Shellz, welcome! Sorry to hear about the news right before your birthday.
There are a few people here with RA and chrons, so hopefully they can pipe in here soon. I know NSAIDs can wreck havoc on your system, but since I don't have chrons, I cannot give you any information.
If you are concerned, is there another doctor you can refer to? Do you see a specialist for the chrons that you can defer to?