This is not the place for this discussion. You need to contact an attorney or attorney/professor of ethics to discuss the dilemma. Moreover, you should either withdraw from the investigation unless you are the one being investigate. You should also steer clear of any communications or interactions on Facebook during the investigation to give an appearance of impropriety.
My response herein is an attempt to give you general information and direction and is not intended to constitute an attorney-client relationship as perceived by state law.
It is per se imprudent for the commanding officer (or any investigating officer) of an Internal Affairs unit to be friending on social media with officers within the department. The lack of judgment in such conduct is staggering, but it is not a conflict of interest as the law defines conflicts of interest. I choose to believe that the command structure of the department does not know about this, assuming that the factual premise of your post is true and verifiable.
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It is certainly a possibility that it is a conflict of interest. But, this is not a legal question on ethics, but rather an issue for internal affairs of the police department to investigate.