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For a given piece of music, there often exist multiple versions belonging to the symbolic (e.g., MIDI representations), acoustic (audio recordings), or visual (sheet music) domain. Each type of information allows for applying specialized, domain-specific approaches to music analysis tasks. In this paper, we formulate the idea of a cross-version analysis for comparing and/or combining analysis results from different representations. As an example, we realize this idea in the context of harmonic analysis to automatically evaluate MIDI-based chord labeling procedures using annotations given for corresponding audio recordings. To this end, one needs reliable synchronization procedures that automatically establish the musical relationship between the multiple versions of a given piece. This becomes a hard problem when there are significant local deviations in these versions. We introduce a novel late-fusion approach that combines different alignment procedures in order to identify reliable parts in synchronization results. Then, the cross-version comparison of the various chord labeling results is performed only on the basis of the reliable parts. Finally, we show how inconsistencies in these results across the different versions allow for a quantitative and qualitative evaluation, which not only indicates limitations of the employed chord labeling strategies but also deepens the understanding of the underlying music material.