I have a BIND DNS Setup with several closely similar, yet different zone files with custom 'views' enabled. Is there a way I can log or find from which zone file [in the hundreds of zone files] has the query been answered?
From none of them; all zone data is in memory.
Once the zones are loaded (on startup and/or reload), the files are no longer referenced.
Of course, BIND logs both the query source address (the client) and the response source address (the view's IP) - you could conceivably correlate these with your knowledge of the zone and view layout.