if ($alphabet{$s} % 2) {
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The problem must be here somehow, becase you're using the % operator only here. The warning indicates that one operand of % is undefined. 2 is a defined constant, so $alphabet{$s} must be undef. %alphabet mus have been filled somehwere else, you didn't show that code, $s comes from a very "ugly" part of your code:

foreach $record (@contents)  {
# where does @contents come from?
# you said a flat-file: why did you read the whole
# file into an array, if you did? is that neccessary?
# you'll probably rather like

while(defined(my $record = <$flatfilehandle>)){
    
    @fields = split(/\|/,$record);
# @fields is global? probably not
    my @fields = split...

    $tidm=$fields[0];$tidm=~s/\s+$//g;
    $nice=$fields[1];$nice=~s/\s+$//g;
#it's much easier to say
 my ($tidm,$nice) = split /\|/,$record;
# and it's more effective to drop the /g, for it's 
# completely useless: You cannot mach the EOString more 
# than one time. Correct me if these variables might 
# contain multiple lines, but i'm "quite sure" they don't 
# :)

    $s = substr($nice,0,1);
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So now $s holds the first character of $nice. If $nice is empty, $s will be empty, too. Do you have the key '' in your hash %alphabet. $s may be any character (apart from '') depending on the input, are all cases covered in %alphabet? If not, consider assuming a default:

(defined $alphabet{$s} ? $alphabet{$s} : 0) % 2
# use exists() if all values of %alphabet are defined
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