Sorry, I don't download random files, especially spreadsheets -- Excel just doesn't have enough security.

poj++ is probably right: if you want to copy one spreadsheet to another, and then just change a couple of things, OLE is probably the way to go.

However, if you want to understand what you're missing, and what's going wrong:

• Since you're hardcoding border => 1, as I pointed out, that possibly explains the "missing vertical borders" (well, maybe not, since that should presumably set all borders the same...)
• My gut reaction to why some cells are copying formats correctly, and others not: the Spreadsheet::WriteExcel ->add_format() method creates a new ::Format object, even if all the parameters match. I am wondering if maybe there is a limit to the number of ::Format objects that can be added before there is loss of information.
• For a full comparison of what's different between the two spreadsheets, after your $workbook->close(), I would instantiate another parser, this time for 'new.xls', and then do a cell-by-cell comparison of the properties for old vs new, using something like Data::Dump's dd() make sure you aren't omitting critical parameters (example code not tested):

  ... # your code above here
  ## Housekeeping
  
  $workbook->close() or die "Error closing file: $!";
  
  close(PROP);
  
  {   ## COMPARISON
      use Data::Dump qw/dd dump/;
      my $old_ws_parse = $worksheet_parse;  # copy to new name for symme
  +try, below
      my $new_wb_parse = $parser->parse( 'new.xls' ) or die $parser->err
  +or(), "Error processing new workbook parse.\n";
      my $new_ws_parse = $new_wb_parse->worksheet( 'Sheet1' );
      open(my $compare_fh, '>', 'compare_formats.txt') or die "compare_f
  +ormats.txt: $!";  # get in the habit of using lexical filehandles
      for my $row ( $row_min .. $row_max ) {
          for my $col ( $col_min .. $col_max ) {
              my $oldcell = $old_ws_parse->get_cell($row,$col) or next;
              my $newcell = $new_ws_parse->get_cell($row,$col) or next;
              # to STDERR
              dd 'oldformat => ', my $oldformat = $oldcell->get_format()
  +;  # you could use Data::Dump::dump() instead, if you want to print t
  +o your own file (similar to
              dd 'newformat => ', my $newformat = $newcell->get_format()
  +;
              # to file handle
              print $compare_fh 'oldformat => ', dump($oldformat), "\n";
              print $compare_fh 'newformat => ', dump($newformat), "\n";
          }
      }
  }
  exit;
  [download]

  (or, if you used a separate filehandle for old and new for this output, you could use diff or similar utility to quickly find the differences
• At some point, you may need to dd on the Spreadsheet::WriteExcel object or sub-objects as well, to see if you can figure out when data is getting corrupted while doing the writing.

But, really, based on your statement "I'm really only going to be changing some of the values of a cell, as well as font color and the fill color of the cell - that's all I'll ever need to change.", I really think you should just follow poj's advice.