I sure wish I could answer this....some say it means you simply have Non-Celiac Gluten Intolerance...some say you have Celiac Disease that has not yet caused enough damage to release enough antibodies to test positive from the digestive tract to the blood.
For me - I tested barely positive on all antibodies at age 43 with total villi atrophy -- celic symptoms had been present my entire life - I just never knew to look for it and doctors dismissed me because I "looked" healthy and all the blood tests they chose to run where normal -- except extremely low iron from age 18. My kids all tested negative at my dx (except for the eldest's DGP) yet all have had much improved health gluten free. Are they Celiac or NCGI -- really doesn't matter the label - they cannot eat gluten and some other foods for a some of them.
Much research is needed in the areas of all digestive and autoimmune disorders -- until research catches up -- sadly we will have many unanswered questions.
For now...since you have had all the proper testing -- given your symptoms and cellular changes in the small intestine -- I would not wait until you test positive or have proof in subsequent biopsy to remove gluten and start healing. There is another way to look at this -- you can remove gluten -- if you improve have another endo at a year and see if the endo provides samples that have no lymphocytes -- also retest your full antibody panel and nutrients at the same time -- if all improved that is pretty clear that you caught Celiac Disease before it ruined your life
Thank you! You are the best!!!