No one route of passenger air transportation now passes over the eastern regions of Ukraine: this can be said for sure. Most of the flights from Moscow to Turkey now skirted closed airspace from the east, thus not flying at all over the territory of Ukraine.

However, airliners fly over the central and western part of the country, especially on the route Moscow-Istanbul (otherwise it would have to fly almost a third longer). Mostly it's boards of foreign airlines, but Russian ones also meet, albeit on rare occasions