I don't read series books as a rule so I don't have this issue but I think if I did what I'd do is prefix the title with some sort of identifier. Something like "HP19-Harry Potter Marries the Hulk".
A long time ago when I was listening to audiobooks on MP3 players I'd break up the files into 14 minute segments and name them like that. This was in the days before MP3 players had reliable resume or bookmark features. It let me sort them in order.
Not quite the same thing, i know, but it would work for books in series, too.
Barry
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