For what it is worth, a book synced from the Kobo Store is stored in the kepub directory inside the .kobo directory with a filename reminiscent of a GUID. Sideloading a book with the same name will result in a second entry in the database. If you sideload epub, it's easy enough to tell between EPUB, KOBO EPUB, KOBO PLUS and OVERDRIVE in the Books view. Sending kepubs does result in a book showing as KOBO EPUB but the details pain will show the path to the book (not to mention sideloaded books missing the Reviews and Related tabs in the View Details
I have never seen an issue where a synced book and a sideloaded book interfered with the other versions reading position, finished or other statistics.
A bit of quick testing did not remove a synced book or a sideloaded book when the alternate version was removed.
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