As for basic issues, you cannot edit a file directly from Perl. You (generally) have to:

1. Open a filehandle to read the file
2. Read the file into some data structure
3. Close the read-only filehandle
4. Edit the data structure
5. Open a filehandle to overwrite the file
6. Write the data structure to the file
7. Close the write-only filehandle

I suspect you're missing the first close and second open. That's a common mistake among newbies. To match the above 7 steps to your needs, you'll need to repeat steps 1-3 for both files.

This sort of does something close to what I think you described. The are a couple of obvious (from the output) errors, but the basic mechanisms are there. As supplied it generates some dummy data into two files 'old' & 'new' and the processes them.

This isn't simple code and will require you to read the comments and code carefully and do some research to understand it given your breif flirtation with perl, but hopefully it will give you a running start.

#! perl -slw
use strict;
use Tie::File;


## Initialise the filenames here
my( $old, $new ) = ( 'old', 'new' );

## Comment this out, once you specify your real files above!!
genTestData( $old, $new );

## Use the files as arrays. See Tie::File.
tie my @old, 'Tie::File', $old;
tie my @new, 'Tie::File', $new;

## Build a lookup table into the old array (file)
## keyed by the catenation of fields 2, 3 & 6;
my %old;
$old{ join $;, ( split "\t", $old[ $_ ] )[ 2, 3, 6 ] } = $_ for 0 .. $
+#old;

## Remove duplicates from the new file, if any.
## Not sure if this was a requirement, your wording was ambiguous.
my %seen;
@new = map{ 
    ++$seen{ join( $;, (split '\t' )[ 2, 3 ,6 ] ) } == 1 
    ? $_ : () 
} @new;


## Now process the new file line by line
for my $lineno ( 0 .. $#new ) {

    ## Split the TSV data into an array.
    my @fields = split "\t", $new[ $lineno ];

    ## And strip the quotes from the partno for later.
    $fields[0] =~ s["([^\x22]*)"][$1];

    ## Catenate the 3 key fields and do a lookup in the old data table
+.
    if( exists $old{ join $;, @fields[ 2, 3, 6 ] } ) {

        ## If it exists, edit the line if the old file
        $old[ $old{ join $;, @fields[ 2, 3, 6 ] } ]

            ## locate the notes field
            =~ s[ ("[^\x22]*") (?= (?: \t [^\t]*? ){2}$ ) ]
                {
                    ## Make a modifiable copy
                    my $notes = $1;

                    ## and append the partno to it
                    $notes =~ s[(?<=")(.*)(?=")][$1:$fields[0]];

                    ## And return the modified field for substituition
                    ## into the old file record.
                    $notes;
                }xe;
        print "Updating old line ", $old[ $old{ join $;, @fields[ 2, 3
+, 6 ] } ];
    }
    ## Else append  the new record to the old file
    ## prefixed with an 'A'
    else {
        push @old, 'A' . $new[ $lineno ];
        print "Adding new line '", $new[ $lineno ], "' to old file";
    }
}

exit(0); ## This updates the files to disk and closes them.

## Everything from here is for generating test data.
sub genTestData {
    my( $old, $new ) = @_;
    srand( 1);
    open OLD, '>', $old or die $!;
    print OLD genLine() for 1 .. 100;
    close OLD;
    open NEW, '>', $new or die $!;
    print NEW genLine() for 1 .. 20;
    close NEW;
}

sub genLine{
    join "\t", map{ '"' . $_ . '"' }
        10000 + int rand 90000,
        'dummy',
        ('l','r')[ rand() < 0.5 ] . int rand(9),
        ('l','r')[ rand() < 0.5 ] . int rand(9),
        'notes',
        'dummy',
        '';
}

__END__
P:\test>295919.pl8
Adding new line '"13471"        "dummy" "r1"    "r1"    "notes" "dummy
+" ""' to old file
Adding new line '"65827"        "dummy" "l8"    "r7"    "notes" "dummy
+" ""' to old file
Updating old line "31648"       "dummy" "l8"    "r8"    "notes:68098" 
+  "dummy" ""
Adding new line '"69773"        "dummy" "r5"    "l3"    "notes" "dummy
+" ""' to old file
Adding new line '"94869"        "dummy" "l5"    "l2"    "notes" "dummy
+" ""' to old file
Adding new line '"45724"        "dummy" "r0"    "l1"    "notes" "dummy
+" ""' to old file
Updating old line "97885"       "dummy" "r5"    "r1"    "notes:16325" 
+  "dummy" ""
Updating old line "95152"       "dummy" "l4"    "l6"    "notes:24029" 
+  "dummy" ""
Adding new line '"49715"        "dummy" "l3"    "l5"    "notes" "dummy
+" ""' to old file
Adding new line '"27962"        "dummy" "l7"    "r8"    "notes" "dummy
+" ""' to old file
Adding new line '"26677"        "dummy" "l5"    "r5"    "notes" "dummy
+" ""' to old file
Adding new line '"73764"        "dummy" "r2"    "r3"    "notes" "dummy
+" ""' to old file
Updating old line "90568"       "dummy" "l6"    "l3"    "notes:90576" 
+  "dummy" ""
Adding new line '"45765"        "dummy" "l2"    "r5"    "notes" "dummy
+" ""' to old file
Updating old line "75975"       "dummy" "l6"    "l6"    "notes:41819" 
+  "dummy" ""
Adding new line '"22538"        "dummy" "r2"    "l8"    "notes" "dummy
+" ""' to old file
Adding new line '"43104"        "dummy" "l0"    "l1"    "notes" "dummy
+" ""' to old file
Adding new line '"56614"        "dummy" "l3"    "l0"    "notes" "dummy
+" ""' to old file
Adding new line '"17160"        "dummy" "r0"    "r2"    "notes" "dummy
+" ""' to old file
Adding new line '"72753"        "dummy" "r3"    "r6"    "notes" "dummy
+" ""' to old file
[download]

Good luck.

#!/usr/bin/perl

my $filename02 = "unapproved.txt";
my $filename03 = "approved.txt";
my $filename04 = "compared.txt";

open(UNAPPROVED,"+<$filename02") || die "Can't open file $filename02";
+ # open destination text file
open(APPROVED,"+<$filename03") || die "Can't open file $filename03"; #
+ open destination text file
open(COMPARED,"+>$filename04") || die "Can't open file $filename04"; #
+ open destination text file

my @unapprovedline;
my @approvedline;

@approvedall = <APPROVED>;
@unapprovedall = <UNAPPROVED>;

close APPROVED;
close UNAPPROVED;

$numoflines01 = @unapprovedall;
$numoflines02 = @approvedall;

for ($x = 0; $x < $numoflines01; $x++) {

    $line01 = @unapprovedall[$x];
    @unapprovedline = split (/\"/, $line01);

    for ($y = 0; $y < $numoflines02; $y++) {
        $line02 = @approvedall[$y];
        @approvedline = split (/\"/, $line02);

        $uleft = @unapprovedline[5];
        $aleft = @approvedline[5];
        $uright = @unapprovedline[7];
        $aright = @approvedline[7];
        $uping = @unapprovedline[13];
        $aping = @approvedline[13];

        if ($uping eq $aping && $uleft eq $aleft && $uright eq $aright
+) {
            print COMPARED "\"", @approvedline[1], "\"", "\t";
            print COMPARED "\"", @approvedline[3], "\"", "\t";
            print COMPARED "\"", @approvedline[5], "\"", "\t";
            print COMPARED "\"", @approvedline[7], "\"", "\t";
            print COMPARED "\"", "@approvedline[9] @unapprovedline[1],
+", "\"", "\t";
            print COMPARED "\"", @approvedline[11], "\"", "\t";
            print COMPARED "\"", @approvedline[13], "\"", "\t", "\n";

        }
        else {
            print COMPARED "\"", @unapprovedline[1], "\"", "\t";
            print COMPARED "\"", @unapprovedline[3], "\"", "\t";
            print COMPARED "\"", @unapprovedline[5], "\"", "\t";
            print COMPARED "\"", @unapprovedline[7], "\"", "\t";
            print COMPARED "\"", @unapprovedline[9], "\"", "\t";
            print COMPARED "\"", @unapprovedline[11], "\"", "\t";
            print COMPARED "\"", @unapprovedline[13], "\"", "\t", "\n"
+;

        }
    }
}

close COMPARED;


# delete UNAPPROVED
[download]

Heres the file that is produced from the above code...

"A1000000"    ""    "DB50F-LEFT"    "DB50F-RIGHT"        ""        "" 
+   "L1:R1 L2:R2 L3:R3 L4:R4 L5:R5 L6:R6 L7:R7"    
"M50DFFU"    ""    "DB50F-LEFT"    "DB50F-RIGHT"        " 1000000,"   
+ ""    "L1:R1 L2:R2 L3:R3 L4:R4 L5:R5 L6:R6 L7:R7"    
"A1000000"    ""    "DB50F-LEFT"    "DB50F-RIGHT"        ""        "" 
+   "L1:R1 L2:R2 L3:R3 L4:R4 L5:R5 L6:R6 L7:R7"    
"A1000000"    ""    "DB50F-LEFT"    "DB50F-RIGHT"        ""        "" 
+   "L1:R1 L2:R2 L3:R3 L4:R4 L5:R5 L6:R6 L7:R7"    
"A1000000"    ""    "DB50F-LEFT"    "DB50F-RIGHT"        ""        "" 
+   "L1:R1 L2:R2 L3:R3 L4:R4 L5:R5 L6:R6 L7:R7"    
"P000001"    ""    "DB9F-LEFT"    "DB9F-RIGHT"        " 5000001,"    "
+"    "L1:R1 L2:R2 L6:R6"    
"A5000001"    ""    "DB9F-LEFT"    "DB9F-RIGHT"        ""        ""   
+ "L1:R1 L2:R2 L6:R6"    
"A5000001"    ""    "DB9F-LEFT"    "DB9F-RIGHT"        ""        ""   
+ "L1:R1 L2:R2 L6:R6"    
"A5000001"    ""    "DB9F-LEFT"    "DB9F-RIGHT"        ""        ""   
+ "L1:R1 L2:R2 L6:R6"    
"A5000001"    ""    "DB9F-LEFT"    "DB9F-RIGHT"        ""        ""   
+ "L1:R1 L2:R2 L6:R6"    
"A9999999"    ""    "DB00F-LEFT"    "DB00F-RIGHT"        ""        "" 
+   "L1:R1 L3:R3 L4:R4 L6:R6"    
"A9999999"    ""    "DB00F-LEFT"    "DB00F-RIGHT"        ""        "" 
+   "L1:R1 L3:R3 L4:R4 L6:R6"    
"A9999999"    ""    "DB00F-LEFT"    "DB00F-RIGHT"        ""        "" 
+   "L1:R1 L3:R3 L4:R4 L6:R6"    
"A9999999"    ""    "DB00F-LEFT"    "DB00F-RIGHT"        ""        "" 
+   "L1:R1 L3:R3 L4:R4 L6:R6"    
"A9999999"    ""    "DB00F-LEFT"    "DB00F-RIGHT"        ""        "" 
+   "L1:R1 L3:R3 L4:R4 L6:R6"
[download]

And this is what i im trying to do with the results produced above...again this is probably a very long way of solving this problem but i cant really think of any other way to do it as my perl knowledge is limited

# for each line, get the part no., compare to contents of 
# the notes field on every other line, if it is in the
# notes field, delete the line otherwise leave and move on
# to the next line.  Finally delete all dupes and merge the
# list with the approved.txt

open(COMPARED,"+<$filename04") || die "Can't open file $filename04"; #
+ open destination text file

@comparedall = <COMPARED>;
$numoflines03 = @comparedall;

for ($a = 0; $a < $numoflines03; $a++) {

    $line03 = @comparedall[$a];
    @comparedline = split (/\"/, $line03);

    $part = @comparedline[1];

    $notes = @comparedline[9];
    @notes = split (/\,/, $notes);
    $numofnotes = @notes;

    for ($b = 0; $b <= $numofnotes; $b++) {
                
        $notescontent = @notes[$b];
        print $notescontent, "\n";

        if ($part eq $notescontent) {
            print "hello";
        }
        

    }
}
[download]

Thanks for everyones help, Steve.