In D779n13, there is no obvious instance of this kind of event, but Kielian-Gilbert's categories do give interesting results when applied to one crucial, "generative" moment and its varied repetitions in subsequent phrases, the result being what she calls an “oscillation” between ii6 and IV. The C# dissonance in measure 3 clearly belongs to a 7-6 suspension figure that stretches from the firmly established tonic triad of measures 1-2 to the ii6 chord in measures 3-4 (see the top system of the graphic below). The inversion of clichéd voice leading in the upper voices—see the top system, middle, combined with the firm bass motion from ^1 to ^4, however, enables a possible reading of a 7-8 suspension against subdominant harmony (top system, righthand side).
By the time the opening phrase reappears after the C# major section, the force of the tonic key is nearly attenuated: if ii6 was more difficult to hear in measure 12, it is all the more difficult in measure 31, after two measures of an A7 chord that is equally plausible as a German Sixth chord in C# major (bottom system). Now the subdominant seems much stronger, even to the point of raising the question whether the resolution to B5 does not invoke a triad with an added sixth (dominant ninth chords do arise accidentally over V7-I progressions in waltzes of the 1820s, but the added sixth is exceedingly rare before its appearance in French and Austrian ballet, operetta, and dance music in the 1860s). If one can indeed hear this moment as a triad with added sixth, then the implications for voice leading are again strong, as the added sixth would lead upward to C# in a return to I or would be stationary in a move to V.
Over the course of the waltz, then, the translational parallelisms of voice leading motives in the phrase openings can be heard gradually to undermine the stability, not of the prolongation (the subdominant function can be served equally well by ii or IV) but of the voice leading implications. The hegemony of the suspension-led motions is not so secure as it seemed. I would argue that, by measures 29-32, we do oscillate between one hearing and the other, first favoring IV (because of its applied dominant), and only later ii (because of the expanded context that ties the subdominant function into the cadence progression).
References:
Jackson, Timothy. "Diachronic Transformation in a Schenkerian Context: Brahms's Haydn Variations." In Carl Schachter and Hedi Siegel, eds. Schenker Studies 2, 239-75. Cambridge: Cambridge University Press 1999.
Kielian Gilbert, Marianne. "Interpreting Schenkerian Prolongation." Music Analysis 22/1-2 (2003): 51-104.