It looks like you are trying to write all rows from all sheets from all input files into one sheet in one output file. The reason you are overwriting data is that you don't increase the row counter between sheets. You need to create a row_count variable outside of all your foreach loops. Then you need to increment it after each write. Maybe something like this UNTESTED: 
use Spreadsheet::XLSX;
use Excel::Writer::XLSX;

(@file_list) = glob "*xlsx";
my $workbook = Excel::Writer::XLSX->new('Target.xlsx');
$worksheet = $workbook->add_worksheet();

my $row_count = 0;
foreach my $setoffiles (@file_list) {
    my $excel = Spreadsheet::XLSX->new("$setoffiles");
    foreach my $sheet ( @{ $excel->{Worksheet} } ) {
        $sheet->{MaxRow} ||= $sheet->{MinRow};
        $sheet->{MaxCol} ||= $sheet->{MinCol};
        foreach my $row ( $sheet->{MinRow} .. $sheet->{MaxRow} ) {
            foreach my $col ( $sheet->{MinCol} .. $sheet->{MaxCol} ) {
                my $cell = $sheet->{Cells}[$row][$col];
                if ($cell) {
                    $worksheet->write( $row_count, $col, $cell->{Val} 
+);
                    $row_count++;
                }
            }
        }
    }
}

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In reply to Re: Merging worksheets in .xls in one Excel sheet by toolic
in thread Merging worksheets in .xls in one Excel sheet by machirajun

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