Hey, I was on the Atkins diet about ten years ago also. I lost 45 pounds on it. But then I had children and you know the story. I choose to fast for health reasons and spiritual reasons as well as weight loss. (It is an added benefit)
The way I look at it when people were more healthy on this earth they ate alot of fish and fruit and vegetables. I think that too much of anything is bad for you, but God would not have put the fresh fruits and vegetables on this earth if they were bad for you.
Your body needs time to get used to changes, so look at the overall picture. If your long term goal is to be healthy and have a healthy body, then clean it out. (Which is exactly what you are doing). Then restart so to speak with an overall healthy look at food.
I struggle with a healthy look at food myself, so fasting is a great way to get that in control.