Yes, studies have shown this as a possible side effect of staying low carb long term. Ketogenic diets are used for epileptic children and they are kept on this diet (without carbups of course) for up to 3 years at a time. All of the studies have used these (and not dieter or atheletes) as models. Their protein intake is much lower than ours so its difficult to make a good comparison.
Regardless, it's best to think of this diet as a shorter term solution. I personally would not run this for more than 12 weeks.
Here is some specific info:
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There are few studies of the long term effects of a ketogenic diet. One of the few, which followed two explorers over a period of 1 year was done almost 70 years ago (1). Beyond that
study, the two models most often used to examine the effects of the ketogenic diet are the Inuit and pediatric epilepsy patients. Epileptic children have been studied extensively, and are kept in ketosis for periods up to three years. In this group, the major side effects of the ketogenic diet are
elevated blood lipids, constipation, water-soluble vitamin deficiency, increased incidence of kidney stones, growth inhibition, and acidosis during illness.
However, the pediatric epilepsy diet is not identical to the typical ketogenic diet used by dieters and healthy adults, especially in terms of protein intake, and may not provide a perfect model. While studies of epileptic children give some insight into possible long term effects of a ketogenic diet, it should be noted that there are no studies of the long-term effects of a CKD or similar diet approach. The consequences of alternating between a ketogenic and non-ketogenic metabolism are a total unknown. For this reason, it is not recommended that a CKD, or any ketogenic diet, be followed indefinitely.