I've had GERD since I was in my early 20's (maybe even earlier), but did not get Crohn's until around the age of 45. Over the years, I've had to take stronger and stronger anti-reflux medications, and now I'm on a proton-pump-inhibitor called Zegerid.
I recently had a small bowel resection due to severe stricturing of my terminal ileum, and for several months prior to my surgery, I noticed that my GERD was the worst it's ever been. I was even eating low residue, low fiber, and extremely bland foods, yet I still had severe problems. I even slept sitting up (in a recliner) for 5 months prior to my surgery.
Since my surgery for the stricturing, my GERD seems to have settled down somewhat, but I'm sure I'll be on PPIs for life.
So, a short answer is that I think a Crohn's flare can make GERD worse.
I forgot to mention that raising the head of your bed with a 2x4 may help...all of my GIs over the years recommended it and it really does help me.
Keeper, I have heard about the side effects of PPIs recently also, but the pain associated with the acid reflux is worse to me than the risk of osteoporosis. I take calcium and vitamin D daily. I have very little fat in my diet and tried acidolpholis (sp.?) but it didn't seem to help. With all of the side effects that go along with biologicals and other crohn's drugs, the risks of PPIs seem very little to me. But, that's just my opinion.