This is my first ever attempt at non-ascii processing, so I'll let the more experienced Monks criticize if this is the wrong approach, or if there's a better one.

After a very quick dig online, I found that setting binmode on all the file handles can fix the issue:

Input file:

$ cat in.txt
}cýæu}*]…‘¦å
hello ›ÇÁ
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Code:

use warnings;
use strict;

open my $fh, '<', 'in.txt'
  or die $!;

open my $wfh, '>', 'out.txt'
  or die $!;

binmode $fh, ":utf8";
binmode $wfh, ":utf8";
binmode STDOUT, ":utf8";

while (<$fh>){
    chomp;
    print $wfh "file: $_\n";
    print "stdout: $_\n";
}
[download]

Output:

# output file
file: }cýæu}*]…‘¦å
file: hello ›ÇÁ

# stdout
stdout: }cýæu}*]…‘¦å
stdout: hello ›ÇÁ
[download]