#!/usr/bin/perl

use 5.12.0;

my ( $file1, $file2 ) = qw( 1.txt 2.txt );

my %seen;

for my $file ( $file1, $file2 ){
    open my $fh, '<', $file
      or die "Can't open file $file: $!";

    while ( my $line = <$fh> ){
        chomp;
        next if $line !~ /RC=?\d{4}\s+/;
        $line =~ s/RC=/RC/;
        $line =~ /(RC\d{4})\s+/;
        my $string = $1 if $1;
        $seen{ $string } = $line;
    }

    close $fh;
}

for my $key ( keys %seen ){
    say $seen{ $key };
}

##</code><code>##

This is line RC0003 in file 2.
This is line RC0001 in file 2.
This is line RC0002 in file 1
This is line RC0004 in file 2.

##</code><code>##

This is line RC0001 in file 1
This is line RC0002 in file 1
This is line RC0003 in file 1

##</code><code>##

This is line RC=0001 in file 2.
This is line RC=0003 in file 2.
This is line RC=0004 in file 2.