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#!/usr/bin/perl

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

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.

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

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