#!/usr/bin/perl
use Modern::Perl; #does an implict use strict; use warnings and activates "new" features
no warnings qw /uninitialized/;

my @result;

{ 
    open my $INPUTFILE, '<', '/Users/ts/input.txt' or die "File error: input file: $!";
    while (<$INPUTFILE>) {
        chomp; 
        my ($index, $value) = split /\t/; 
        $result[$index] = $value;
    }
} 

{ 
    open my $OUTPUTFILE, '>', '/Users/ts/output.txt' or die "File error: output file: $!";
    while (my ($index, $value) = each @result) {
        next if $value > 500;
        say $OUTPUTFILE, "$index\t$value"; 
    }
} 

input.txt
1 10
2 11
3 9
4 500
5 550
etc