One way to do it is to create another hash to map the parts to the key:

my %table;
my %map;

foreach my $key (sort keys %Data)
{
    my $lValue = $Data{$key};
    my @array = split ' ', $lValue;
    my $lPartStart = $array[2];
    my $lPartEnd = $array[4];
    my $lReference = $array[8];
    chop($lReference);
    $table{$lReference} = [] unless exists $table{$lReference};
    push @{$table{$lReference}}, $lPartStart;
    $map{$lReference}{$lPartStart} = $key; # THIS LINE ADDED
}

foreach my $lReference (sort keys %table)
{
    print "Ref: $lReference, parts: ";
    my @parts = @{$table{$lReference}};
    print join ', ', sort @parts;
    print "\n";
}
foreach my $lReference (sort keys %table)
{
    print "Ref: $lReference, lines: ";
    my @parts = @{$table{$lReference}};
    my @lines = map { $map{$lReference}{$_} } sort @parts;
    print join ', ', @lines;
    print "\n";
}
[download]

Output:

Ref: 1, parts: 1, 2, 3
Ref: 2, parts: 2, 3, 4
Ref: 1, lines: 5, 4, 6
Ref: 2, lines: 17, 18, 16
[download]

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