This is a problem in general, not a good way to handle it anywhere. It was two separate episodes when aired on TV (even if aired 'back to back', but on the redistribution it was made one single continuous video.
You can either manually split it, like you did - but typically you would never watch the 2nd half of these without the first part for continuity sake.
What I do is give it an episode number of "16-17", then populate the tag data with S16 info and manually paste in any relevant S17 data as needed to the appropriate tags (like name/description).
My worst example of this is the first episodes of Stargate Universe. The first episodes (titled 'Air') were originally broadcast as 3 separate episodes (Air (1), Air (2), and Air (3)) but is really one long episode. In my library the filename for that one is "Stargate Universe.S01E01-02-03.2009-10-02.Air (1-3).mkv" with the episode name "Air (1-3)" and an episode tag of "1-3". The description tag has all three descriptions from TVDB as three separate paragraphs.
The nice thing about MC (vs other solutions) is that you have near complete control in how you handle this. Do what makes sense to you.