I had wondered that also but never took the time to look, until now. Paradox opens all the WinSPM\Data (.db) files. The file with the Site info is, surprise, Site.db. I opened it in Paradox, shuffled the site names around and saved. Next, opened up WinSPM, connected to one of the changed sites. Surprise again, correct site was identified as it connected but \SiteData ([View] [Browse Reports]) is for the "other" Legend. These are .txt files and remain in the correct subdirectory under WinSPM but somewhere is an index file that is pulling in the "wrong" information. Swapping the .txt files in the subdirs has no effect. So far have found no .db file with the SiteData info. I will change things back around until I get a better handle of how things are structured.
The only fields visible in the Site.db table are SiteID, SiteName, ContactName, ContactPhoneNumber, whereas the table structure info reports 24 fields. Anyway, have fun playing around.