Why don't you fix the bad files instead of having your program handle them? 
#!/usr/bin/perl

# usage:
#    rem_surrogate.pl < infile > outfile

use strict;
use warnings;

binmode STDIN;   # Disable :crlf
binmode STDOUT;  # Disable :crlf

my $read_size = 16*1024;

my $buf = '';
for (;;) {
   my $rv = read(STDIN, $buf, $read_size, length($buf));
   die("$!\n") if !defined($rv);
   last if !$rv;

   $_ = substr($buf, 0, int(length($buf)/2)*2, '');
   s/\G(.)(?:[\xD8-\xDF]|(.))/
      defined($2) ? $1.$2 : "\xFD\xFF"
   /esg;
   print;
}
print("\xFD\xFF") if length($buf);

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In reply to Re: Handling malformed UTF-16 data with PerlIO layer by ikegami
in thread Handling malformed UTF-16 data with PerlIO layer by almut

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