When a worksheet is copied to a new workbook, certain cell colors are adjusted to the color palette in the destination workbook, which is a default behavior of MS Excel. These kind of issues raise mostly when merging worksheets of binary file (*.xls) to xml format (*.xlsx), as the binary files completely rely on palette colors.
While copying a worksheet into another workbook, it is recommend to reset the palette of both the workbooks using MS Excel to avoid mismatch in colors. This can be done by resetting the palette in Save Options of workbook as in the below screen-shot. This step must be done in all the workbooks to be merged if the palette is modified.
Reset Workbook Palette
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