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No, I don't think so. One of my sites was totally hi-jacked including the link pages, but Google does not merge the two.
In your case, I find it very weird. I think there must be some unknown connection(s) somewhere between your two sites that trigger Google to merge them.
This has happened to me a few times.It is one way to hijack a site.Of course if you change the content of the original and google lifts the ban off it, it will again see them as different sites.