I'm not sure what your problem is. As in, is it a problem with Anvil, or with the music.
It might be easier all round to have two separate tracks, as in Flute1 and Flute2, but your question suggests there's a problem with this. I don't know why Anvil might object to this, if it does just define the tracks as different names and then set the instrument to Fl1 and Fl2 later. Doing it this way could allow you to get more depth to the sound by using two slightly different flute 'patches'. Or is it that you'd rather NOT split the track, but there's something about bar 22 that Anvil has a problem with - what is being objected to, what does Anvil do.
I've tried entering orchestral scores before - it's VERY tedious work, even if the software is helpful, and most isn't too helpful. It's better if you can 'play' the music in, and record it into midi, but this required some degree of ABILITY which I do NOT have.
I've got a book here 'Classics in Sequence' by William Lloyd and Paul Terry which is very much a 'How-to' book about sequencing Classical pieces (there's a Rock and a General version too. There are various examples, but no Beethoven, but there are places where there's similar structures (i.e. a track for Flutes clearly involving two notes as you're trying to do - but i don't see the same thing with mixed notes and rests. Even so, I don't see why it should be a problem.
Way back - I was using a DOS system called Quick Score Deluxe. I'm sure that was simpler than Anvil. As far as Windows systems are concerned you might try to find MuseScore which allows entry of complete scores, and save as midi - this seems comparable to the QSD I was using rather than being a full-blown DAW type system, but I'm sure there'll be other systems available. I've got MuseScore here, if I understand better what the problem actually is then I could try MS and see what that does, and if that would be a mose useful avenue for you.
Geoff