I wish your Endo had thought to tell you that you needed to stay on gluten. You will need to go back on gluten to ensure that your biopsy is not a false negative. Be aware that there can be false negatives on biopsy even without having stopped gluten for a couple of weeks.
The choice to biopsy is yours to make. It sounds like you have a doctor's diagnosis from your Endo. If you should find that the challenge results in severe symptoms do call the GI doctor's office and let them know. Some of us have more severe reactions to gluten after being gluten free for even a short time.
Glad you have been feeling better and hope you recover quickly from the challenge if you choose to do one.