I appear to have found a bug with the MergeNamedStyles function added recently.  Please run the following top-level code (adjusting the file paths as needed) with the attached zipped workbooks as a .NET 9 C# console app
Dev.zip (790.5 KB)
:
using Aspose.Cells;
Workbook targetWbk = new(@"C:\Swift\Templates\Dev\InputCombined_Stoch.xlsx");
var inputSheet = targetWbk.Worksheets["Input"];
if (inputSheet != null)
{
    targetWbk.Worksheets.RemoveAt("Input");
}
inputSheet = targetWbk.Worksheets.Insert(0, SheetType.Worksheet, "Input");
var greySheet = targetWbk.Worksheets["Grey"];
if (greySheet != null)
{
    targetWbk.Worksheets.RemoveAt("Grey");
}
greySheet = targetWbk.Worksheets.Insert(1, SheetType.Worksheet, "Grey");
var sheet = targetWbk.Worksheets["Map"];
if (sheet != null)
{
    targetWbk.Worksheets.RemoveAt("Map");
}
DeleteStyles(targetWbk);
Workbook srcWorkbook = new(@"C:\Swift\Templates\Dev\Input_STRUCTURE.xlsx");
targetWbk.MergeNamedStyles(srcWorkbook);
static void DeleteStyles(Workbook wbk)
{
    string[] SWIFT_CUSTOM_STYLES = [
            "S_Date",
            "S_Date_Custom",
            "S_Decimal",
            "S_Decimal_Custom",
            "S_General",
            "S_General_Custom",
            "S_Header",
            "S_Header_Custom",
            "S_IDate",
            "S_IDecimal",
            "S_INumber",
            "S_IPercent",
            "S_IText",
            "S_Number",
            "S_Number_Custom",
            "S_ODate",
            "S_ODecimal",
            "S_ONumber",
            "S_OPercent",
            "S_OText",
            "S_Percent",
            "S_Percent_Custom",
            "S_xDate",
            "S_xDate_Custom",
            "S_xDecimal",
            "S_xDecimal_Custom",
            "S_xGeneral",
            "S_xGeneral_Custom",
            "S_xNumber",
            "S_xNumber_Custom",
            "S_xPercent",
            "S_xPercent_Custom"
        ];
    var builtInStyles = Enum.GetNames<BuiltinStyleType>();
    for (var i = 0; i < wbk.CountOfStylesInPool; i++)
    {
        var style = wbk.GetStyleInPool(i);
        if (!builtInStyles.Contains(style.Name) && !SWIFT_CUSTOM_STYLES.Contains(style.Name))
        {
            foreach (Worksheet sheet in wbk.Worksheets)
            {
                for (var r = 0; r <= sheet.Cells.MaxRow; r++)
                {
                    for (var c = 0; c <= sheet.Cells.MaxColumn; c++)
                    {
                        Cell cell;
                        if ((cell = sheet.Cells.CheckCell(r, c)) != null)
                        {
                            if (cell.IsStyleSet && cell.SharedStyleIndex == i)
                            {
                                cell.SetStyle(wbk.DefaultStyle);
                            }
                        }
                    }
                }
            }
        }
    }
    wbk.RemoveUnusedStyles();
}