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my ($i, %seen) = (0);

my @no_dup =
...
    @with_dup;

@no_dup = map { 2 < @$_ ? $no_dup[$_->[0]] : () } values %seen;

my ($i, %seen) = (0);

my @no_dup =
...
    @with_dup;

@no_dup = @no_dup{grep $_ != -1, values %seen};