If your file is small, just read it into an array first:

open F, $file or die $!;
my @data = <F>;
for my $i ( 0..$#data ) {
    if ( $i == 0 or $i == $#data ) {
        #first or last line so do whatever
        print $data[$i];
    }
    else {
        # not first or last line
        $data[$i] =~ s#^(\d{16})#$_ = $1; tr/0-9/A-J/; $_#e
        print $data[$i];
    }
}
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