The only suitable answer to the question: "What were you doing when I called you?", would be "Estaba comiendo". If you answered: "Estuve comiendo", I would kind of... understand that you were having lunch, but trust me, not even one native speaker would answer like that. Estuve comiendo is more like something that you did earlier that day or the day before. I will give you an example: If you asked me: What did you do yesterday? I would answer: Estuve viendo videos en Internet. (I watched videos on the internet) In this case I would not use past continuous, but past simple.

The only suitable answer to the question: "What were you doing when I called you?", would be "Estaba comiendo". If you answered: "Estuve comiendo", I would kind of... understand that you were having lunch, but trust me, not even one native speaker would answer like that. Estuve comiendo is more like something that you did earlier that day or the day before. I will give you an example: If you asked me: What did you do yesterday? I would answer: Estuve viendo videos en Internet. (I watched videos on the internet) In this case I would not use past continuous, but past simple.