Can moderate to severe calcium deficiency cause intestinal issues over time? if so, what kind of issues?

Generally not.: prolonged hypocalcemia generally does not cause intestinal problems. It usually causes neuromuscular problems. On the contrary, G.I. problems can often be the cause of low calcium levels, usually from eating disorders, prolonged vomiting, or inappropriate supplementation with magnesium, zinc, or laxatives. Hypocalcemia can be a severe problem, so follow your doctor's advice closely. Good luck.

First things first: My response is another question. Why the low calcium? The answer to this question is more likely related to the GI symptoms.