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They’re fine to on their own, or with other foods. I see no reason why you would need to separate them.
If anything, things like lentils are a good way to make a meal well rounded with protein and fiber.
If you’re dealing with a deficiency, and how to eat to resolve that, that could be well above any kind of advice we can give you over the internet. We don’t know what you’re deficient in, by how much, or why. There could be many reasons for that