> [...] I have confirmed by commenting/uncommenting steps of the
> hinting process that af_glyph_hints_align_edge_points is the
> function that snaps the tilde back to flat, so if my understanding
> is correct, the points at the top and bottom of the tilde are
> forming edges and are being rounded towards each other, causing the
> tilde to remain flat.

Yes, it seems so.  In case you haven't read it already, this article
gives a nice overview, but please be aware that it is 20(!) years old
and thus partially outdated with respect to some details:

  https://www.tug.org/TUGboat/tb24-3/lemberg.pdf

> How should I proceed?

Perhaps you can try to remove the affected segments from the
corresponding edges.  If that fails there is still the possibility to
apply the vertical distortion afterwards...


    Werner

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