<<SPOILER ALERT>>
I think the Unknown might've been referring to the "memories" of Naminé that Sora gains while in Castle Oblivion, and that in order to get those "memories" back he first needed to forget Kairi, which is what the whole story of Chain of Memories hinges on.
We know that the Organization was trying to get Naminé to replace Kairi in Sora's memory, so they could control him, right? I think it would therefore make sense for an Unknown to give Sora that warning at the beginning of Chain of Memories, if for nothing else than him being open to "remembering" Naminé as something dear to him, that we now know to not be true.
So, in a way, we can consider the topic of the Unknown's message as being resolved, if we think it was merely a ploy to get Sora to go to Castle Oblivion and accept the "memories" of Naminé once they are implanted...
<<END SPOILER>>
This make sense to anyone? Sorry if it's been said before, but I just finished COM last night, and I'd been avoiding COM-related topics like the plague until today, to avoid any potential spoilers...