If I have read correctly you are scanning an input file and outputting changed lines only where column 12 is 000015, 000030 or 000060. Column 13 is changed to 92, 46 or 23 and a number of blank columns (8, 4 or 2) starting at 30 are removed.

Since there looks to be a pattern to your changes I have coded them into a hash to avoid the multiple ifs.

#!/usr/bin/perl 
use strict;        
use warnings;    

my $infile  = $ARGV[0];
my $outfile = $ARGV[1] || 'resultfile.txt';

unless (@ARGV) {
  die "Usage: ReplaceNewLine.pl <inputfile> [<outputfile>] \n";
}

open IN, '<', $infile 
   or die "$infile not found in current location";

open OUT, '>', $outfile 
   or die "Cannot open $outfile";
   
# Place header from source file into $header variable
my $header = <IN>;
print OUT $header;

# changes
my %change = (   
  '000015' => [92,30,8],
  '000030' => [46,30,4],
  '000060' => [23,30,2],
);

# enhanced or standard files
my @field = split "~",<IN>;;
my $filetype = $field[14] ? 'Enhanced' : 'Standard';
if ($filetype eq 'Enhanced') {
  
  # process lines
  my $count=0;
  foreach my $line (<IN>) {
    ++$count;
    chomp($line);
    my @field = split "~", $line;        
    if ( exists $change{$field[11]} ) {    
    
      $field[12] = $change{$field[11]}[0];
      my $posn   = $change{$field[11]}[1];
      my $cut    = $change{$field[11]}[2];
    
      my $discard = join '',splice(@field,$posn,$cut);
      warn "Warn : $discard discarded at line $count" if ($discard);
      
      print OUT join '~',@field;
      print OUT "\n";
    }
  } 
  print "$count lines processed from $infile\n";
} 

close IN;
close OUT;
[download]

Note the first 2 lines of input are not processed