The problem is that S::PE::SaveParser uses the deprecated set_merge method instead of the newer merge_range method from Spreadsheet::WriteExcel. SaveParser iterates over all the possible cells in the source file, and it applies set_merge on them at the end of its SaveAs method.

So, I have added the following code to apply merge_range on the destination file, at a place where the module iterates over worksheets in the SaveAs method:

# Merged areas
foreach my $area ( @{ $oWkS->{MergedArea} } ) {

    my $cell = $oWkS->Cell($area->[0], $area->[1]);
    my $oFmtN = $oWrEx->addformat();
    $oFmtN->copy($hFmt{$cell->{FormatNo}});
    $oWrS->merge_range( @$area, $cell->{Val}, $oFmtN, 0);
}
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The thing here is the last '0' in the parameter list for merge_range: If it were a true value, merge_range will treat the value as unicode. Otherwise it won't, according to the docs. So, this '0' shouldn't be hardwired.