I don’t quite understand this. Particularly paragraph 4.
How do you know that logos in a CMYK file are converting to RGB? What tells you about their colour mode? To my way of thinking it’s an impossibility.
Are the logos somehow placed and linked? If so. they should be embedded, in which case they will be in CMYK if they were not already.
Maybe the Color panel is confusing you. Be sure to convert the sliders to the right colour mode with the panel’s fly-out menu.