#!perl -w

use DBI;

# output file 
$newfile = "./output.txt";

# open the new .txt file
open(BATCH, ">>$newfile") || die "Can't open $newfile : the output.txt
+ file. $!";

# sets and prints the system date to the log file
$datestamp = `Date /T`;
print BATCH $datestamp;

# initialize the variable to count the batch lines created
$linecount = 0;

# variable with query to go against xyz.batch_lines table
$asql = "SELECT  batch_line  FROM xyz.batch_lines WHERE exe_c = 'N' ";
$bsql = "UPDATE cscadmin.crs_batch_lines SET exe_c = 'Y' WHERE exe_c =
+ ? ";

# connect to oracle and extract data
my $dbh1 = DBI->connect("dbi:Oracle:CS001", "admin", "admin123");

my $statement = $dbh1->prepare($asql);
     $statement->execute; 
     $statement->bind_columns(\my ($batch_line, $row_id));

$statement->execute();
    while ($newfile= $statement->fetchrow_array) {
        $newfile=~s/p13/p12/g;
            $newfile=~s/D:/\nD:/g;
        # $newfile=~s/\b5%\b/\b5%%\b/g;
        $newfile=~s/%/%%/g;
                      # write to the file
            $timestamp = `Time /T`;
            chop $timestamp;
                       print BATCH $newfile." ".$timestamp;
               # writes to screen
                print $newfile;   
               # counts the batch line being read
        $linecount++;    
    # executes the batch line
       # system($newfile);
        
# Mark batch lines in table as read    
       $statement2 = $dbh1->prepare($bsql);         
       $statement2 ->execute($row_id);
  
 } 

$statement->finish();
$statement2->finish();

# close oracle connection
$dbh1->disconnect();

# print count of batch lines
print BATCH $linecount;

# close new .txt file
close (BATCH);
[download]

#!perl -w

use strict;
use DBI;

# output file 
my $newfile = "./test_output.txt";
open(BATCH, ">>$newfile") || die "Can't open $newfile : the test_outpu
+t.txt file. $!";

# sets and prints the system date to the log file
my $datestamp = `Date /T`;
print BATCH $datestamp;

# initialize the variable to count the batch lines created
my $linecount = 0;

# connection to database
my $dbh = DBI->connect("dbi:Oracle:CS1", "admin", "admin123");
my $sql = "SELECT  batch_line, rowidtochar(rowid)  FROM batch_lines";

my $sth = $dbh->prepare($sql);
$sth->execute();

my ($batch, $row_id);
$sth->bind_columns(\$batch, \$row_id);

my $sth2 = $sth;

my $count=1;

while($sth->fetch()) {
  ##### test print
 # print BATCH "$row_id <$count>";
 # print "$row_id <$batch>\n";
 # $count++;
 #####
   
       $batch=~s/p12/servername/g;
       $batch=~s/D:/\nD:/g;
       $batch=~s/%/%%/g;
    
         # write to the file
         my $timestamp = `Time /T`;
         chop $timestamp;

             ##### test print
             print BATCH "$row_id <$count> $batch"." ".$timestamp;
             #####
             
         #  print BATCH $batch." ".$timestamp;
         #  writes to screen
             print $batch;   
         #  counts the batch line being read
             $linecount++;   
             
             ##### test count
             $count++;
             #####
             
         # executes the batch line
         # system($batch); 
         
    
     ##### update
      print BATCH "\n^^^^^^^^^^^^^^$row_id^^^^^^^\n";
      my $bsql = "UPDATE batch_lines SET exe_c = 'Y' WHERE  exe_c = 'N
+' AND rowid = chartorowid($row_id) ";
      $sth2= $dbh->prepare($bsql);
      $sth2->execute();
     #####
     print BATCH "\n########### $row_id #########\n"
      
}
$sth->finish();
$sth2->finish();

# close oracle connection
$dbh->disconnect();

# print count of batch lines
print BATCH "\nLines extracted this period: ".$linecount."\n";

# close new .txt file
close (BATCH);
[download]

I guess the table doesn't have a primary key? Also you should use RaiseError or else check the status of every DBI statement. Anyway you're probably being redundant by specifying 'where rowid = .. and exe_c = ..'. And you can still use placeholders(psuedocode ahead):

my $dbh = DBI->connect('...', 'user','passwd',
 {PrintError=>0, RaiseError=>1});
my $sql = <<EOT;
select ... from .. where exe_c = 'N'
EOT
my $sel_h = $dbh->prepare($sql);
$sql = <<EOT;
update ... set exe_c = 'N' where rowid = ?
EOT
my $upd_h = $dbh->prepare($sql);
$sel_h->execute;
$sel_h->bind_columns(...);
while ($sel_h->fetch) {
 ...
 $upd_h->execute($rowid);
}
$dbh->disconnect;
[download]

------------
ooo  O\O  ooo tilly was here :,(