Amoebiasis in specific terms refers to e histolytica. Did they find this particular parasite or are they just guessing?
Flagyl is overrated and overused and seldom works and seldom works by itself. Getting a firm diagnosis of the parasite is always helpful so the correct protocol can be implemented.
Your symptoms are saying that the Flagyl did not work, I am sure there is nothing to worry about. Lumicidal drugs such as Paromomycin are usually given along with another agent.