I think, we can use "remain in the dark" when we communicate that we don't have light and are kept being in the dark actually.
But, can we use the phrase as metaphor in the academic paper?
For example, "The mechanism of the phenomenon remains in the dark."
Or, "remains unclear" is better?
For an academic paper I think either
(if you know nothing about it)
The mechanism of the phenomenon is unknown
or
(if you know something but not everything about it)
The mechanism of the phenomenon is not fully understood
would be better.
First, it is the observer of the phenomenon in question who could be described as "in the dark", not the phenomenon itself. People, not things, are in the dark. Second, the phrase is not normally used about scientific or other kinds of factual knowledge in any case, but about the passage of information (or lack of it) between humans. So in politics or in business it's common enough, and often contains an implication that the secrecy is deliberate. People who are "in the dark" are also those who are "out of the loop".
My department is being kept in the dark about the re-structuring.
The government is in the dark about Russian intentions.
The leadership pursued this policy while keeping their followers in the dark.
In a scientific paper about natural phenomena it wouldn't be appropriate to use it at all. Your own suggested replacement, "remains unclear", is a good substitute.
