Harmonic analysis is a creative reductionism and not a mechanical operation. There’s no single valid harmonic analysis. Different scholars perform harmonic analyses differently, and disagreements arise everywhere:
See “On the relative openness of syntax” in Mark Gotham’s paper
As a single example, below are three different analyses of the beginning of Beethoven’s op. 2 no. 1 mov. 1 (🎥 audio on YouTube):
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And how it’s annotated in William E. Caplin’s book:



Christopher White, “The Music in The Data”, chapter 3 on harmony
AugmentedNet paper - also follow other cited works from there