Hello Beany, sorry to hear about your girlfriend. I saw in your other post that she is newly diagnosed? Crohn's can be bery scary and intimidating for everyone involved, you should tell her about this website, we would love to help her through it
Crohn's is a very complicated disease. Basically her immune system doesn't recognize the cells in her digestive tract and sees them as a threat, so it attacks. It is an auto-immune disease. The med she is on, as well as several others, suppress the immune system to try to stop or slow down the immune system from attacking the digestive tract.
I wouldn't say that she is going through the flu, she is probably flaring. A flare does present flu like symptoms like the ones you mentioned, and it can involve a lot more symptoms too. Crohn's is very painful, especially during a flare. If you have any other questions, please feel free to ask, I kind of just gave the over view of it, but like I said, it is a very complicated disease and it can be hard to understand at times