This should get you moving in a useful direction; it demonstrates the use of a Hash (which happens to also be a Hash Of Hashes (HoH), which you could research on your own).

CAVEAT: This is not production quality code. Its purpose is demonstration, not solution.

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

# Set up a hash to receive the information
my %violationdata = ();

# Read the violations file into the hash
open my $violations, '<', 'violations.txt' or die;
while (my $vline = <$violations>) {
    my ($vkey, $ukey, $credit, $debit, $balance, $notes) = 
        split /\s+/, $vline;
    $violationdata{$vkey}{UKEY} = $ukey;
    $violationdata{$vkey}{CREDIT} = $credit;
    $violationdata{$vkey}{DEBIT} = $debit;
    $violationdata{$vkey}{BALANCE} = $balance;
    $violationdata{$vkey}{NOTES} = $notes;
}
close $violations;

# Display the contents of the hash
foreach my $okey (sort keys %violationdata) {
    print "  $okey:\n";
    foreach my $skey (sort keys %{$violationdata{$okey}}) {
        my $sval = $violationdata{$okey}{$skey};
        print "    $skey:  $sval\n";
    }
}

# Now process the waivers and update the hash
open my $waivers, '<', 'waivers.txt' or die;
close $waivers;

# Now write out the hash to the updated violations file
open my $updated, '>', 'updated.txt' or die;
close $updated;
[download]

Results:

$ ./violwaiv.pl
  abcd123:
    BALANCE:  -900.00
    CREDIT:  100.00
    DEBIT:  1000.00
    NOTES:  (VIOLATED)
    UKEY:  klmn123
  abcd124:
    BALANCE:  -900.00
    CREDIT:  100.00
    DEBIT:  1000.00
    NOTES:  (VIOLATED)
    UKEY:  klmn124
[download]