Could a prolonged amount of Antibiotics severely affect the digestion Gut Microbiota?
Yes, even if you will not kill ALL the bacteria in your gut, you can mess up your flora pretty badly by using antibiotics for prolonged time.

For how long? It depends from person to person, from antibiotic to antibiotic. 

Similar to Crohn's disease? Some symptoms like abdominal pain, diarrhoea and weight loss can occur in case of messed-up flora like in Crohn's disease (and many other diseases!).