I am new to this, just read your post. My father has Celiac or something. Has been gluten free for 3 months (very strict, no cross-contamination) still has bad anemia (7.9 Hemaglobin and it has continued to progrees downward rather than in an upward direction ie. 9.4 to 8.4 to 7.9 over the last several months rather than upward.) Never did the small intestinal biopsy for proof and GI's blood test (gliadin IgA AB was barely elevated) while still on regular diet. Huge gastric improvement with gluten-free diet. Most all gastric (IBS-like symptoms) have gone away.
I am very interested that your doctor tested you for Whipple Disease. I think that is very forward thinking since it is such a rare disease. I am especially interested because I think my Dad may have that. He is 84 and it seems difficult to get tests for him since doc's seem to think that it is just his age. Maybe for his doctors his age makes him not so hopeful to cure perhaps. But we are in the process of being referred to a GI doctor that is very familiar with Whipple Disease.
It sounds like you may have a very good doctor to go to the extent to 1.) consider you could have Whipple Disease and 2.) actually test you for it.
How did your tests go? Any sign of Whipple Disease? I hope that your condition has improved since your post.
Any information would be greatly appreciated.