This is true, I was assuming (Big mistake..) that given the leading zeroes that these numbers were all zero padded. If not the following Schwartzian Transform should work- it's just not as simple a fix as the earlier one.

# Note: Read Schwartzian Transforms from bottom-up,
#  it makes it easier to understand that way.
@sorted =
  # And finally map back to the original array.
  # [3,['CCI003','1','N']] -> ['CCI003','1','N'].
  map { $_->[1] }

  # Sort by the numeric component we just extracted
  sort { $a->[0] <=> $b->[0] }

  # Map onto an array consisting of the numeric component
  #  of the first part.
  # ['CCI003','1','N'] -> [3,['CCI003','1','N'].
  map { [ $_->[0]=~/(\d+)/, $_] }

  # Take the initial array
  @array;
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Update: Fixed bad formatting.