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PyUtils: Make sure diff-root syncs properly across event boundaries

Alaettin Serhan Mete requested to merge amete/athena:master-diff-root-more-updates into master

This is a follow-up to !45328 (merged). Here, we improve the re-syncing logic to better handle crossing event boundaries. When events are ordered, we also take advantage of the event numbers to ensure we quite early if they are different between the files.

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