I think that the best way is to load your file into a hash (each IP as a key, the hash value doesn't matter), close the file; then add each IP in your array to the hash (a hash will remoce duplicates anyway); once you've finished that, just write the hash keys (i.e. unique IP addresses) to a file (or to the same file if you're confident that it works OK).

A quick untested example:

open my $IN, "<", $awsLists or die "could not open $awsLists $!";
my %hash = map { chomp; $_ => 1 } <$IN>;
close $IN;
chomp @command; # just in case you need it. Note: you could choose a b
+etter name for your array
$hash{$_} = 1 for @command;     
open my $OUT, ">", "$awsLists.out" or die "could not open $awsLists.ou
+t $!";
print "$_\n" for keys %hash;
close $OUT;
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Using a hash lookup will be usually be much faster than greping your file or its content many times.