not removed with $str =~ s/^\x{feff}//;

compare how the behavior changes with open my $fh, '<:encoding(UTF-8)', '../data/publicextract.charity.json' or die "Unable to read Charity JSON File"; compared to the open line you currently use.

If you want perl to treat the bytes in the file as UTF-8, and thus be able to use s/^\x{feff}/, you have to tell perl to read the file as UTF-8¹. If you want perl to continue to read the file as a series of bytes (not using the UTF-8 encoding), then leave your open as-is, and have your regex instead either search for the three bytes in octal with s/^\357\273\277// or in hex with s/^\xEF\xBB\xBF//.

#!perl

use 5.012; # strict, //
use warnings;
use Devel::Peek;

open my $fo, '>:raw', 'threebytes.bin';
print {$fo} "\xEF\xBB\xBF";
close $fo;

open my $fbytes, '<', 'threebytes.bin';
Dump($_ = <$fbytes>);
printf "length no-encoding: %d bytes\n", length($_);
printf "match no-encoding 3bytes?  %s\n", m/^\xEF\xBB\xBF/ ? 'match' :
+ 'nope';
printf "match no-encoding unicode? %s\n", m/^\x{FEFF}/ ? 'match' : 'no
+pe';
close $fbytes;

open my $futf8, '<:encoding(UTF-8)', 'threebytes.bin';
Dump($_ = <$futf8>);
printf "length utf8: %d characters\n", length($_);
printf "match utf8 3bytes?  %s\n", m/^\xEF\xBB\xBF/ ? 'match' : 'nope'
+;
printf "match utf8 unicode? %s\n", m/^\x{FEFF}/ ? 'match' : 'nope';
close $futf8;

__END__

SV = PV(0x6ac038) at 0xb3ebe0
  REFCNT = 1
  FLAGS = (POK,pPOK)
  PV = 0xb4d308 "\357\273\277"\0
  CUR = 3
  LEN = 81
SV = PV(0x6ac038) at 0xb3ebe0
  REFCNT = 1
  FLAGS = (POK,pPOK,UTF8)
  PV = 0x3442c98 "\357\273\277"\0 [UTF8 "\x{feff}"]
  CUR = 3
  LEN = 10
length no-encoding: 3 bytes
match no-encoding 3bytes?  match
match no-encoding unicode? nope
length utf8: 1 characters
match utf8 3bytes?  nope
match utf8 unicode? match
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