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Please try to clear the data cache and refresh again if you can get correct data.
Regards,
If I understand correctly, you have one or more queries in Power BI Desktop that gets data from Excel tables and if you refresh in Power BI Desktop, some data is missing?
So you did not import the Excel sheet and you don't try to refresh in Power BI (published report).
My best guess is that some data can't be processed as it doesn't meet the format expected by the queries.
E.g. numbers with fractions that were defined as whole numbers, dates in another format.
It may also be that you have column names hard coded in your queries, which typically happens with type changes, reordering or selecting column, (un)pivoting, grouping, expanding and many more. So if columns change in your Excel tables, then you can get unexpected results.
If you can provide some query code, example data that is not processed correctly, actual results and expected results, then we'll be better able to help you.
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