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Mistakes can certainly occur in drafting a paper, and it’s unwise to make accusations before knowing the full story. If you have questions, as a coauthor of the paper, it is reasonable for you to be satisfied that the revised paper is complete and accurate.
You can certainly ask your coworker for clarification without accusing him of altering the original data. If you are worried that he will feel accused in any case, this would also be a question for your mutual advisor. As the PI for this research project (and likely as someone who has refereed many papers as well), your advisor might be in the best position to judge whether the explanation is appropriate.
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