The docs for Spreadsheet::ParseExcel::SaveParser state that the module works "by reading it with Spreadsheet::ParseExcel and rewriting it with Spreadsheet::WriteExcel". So any merged cells will be lost when re-writing. You will need to use the WriteExcel module to re-create the merged cells, which means you will have to separate the reading and writing in your own script.

To merge the cells you use the "merge_range" method with a Format:

my $format = $workbook->add_format( align => 'left' );
$worksheet->merge_range('A1:C1', 'New Value', $format);
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See the docs for Spreadsheet::WriteExcel