The || is being parsed wrong; use another delimiter for your s///. Also you have a couple of typos past that. A corrected version could look like:

my @files = qw(quotePAGE1 quotePAGE2);

for (@files) {
    open IN, $_ or die "failed opening file $_, at";
    $\ = "\n\n";
    my $num = 0;
    my($chunk,$q_num,%s_nums,%auth,@s,%subj);
    while($chunk = <IN>) {
        ++$num;
        $chunk =~ s|^/-a(\S+)[^/n]*\n|| or 
     die "no author?  file $_, chunk $num; at";
        $a = $1;
        while($chunk =~ s{/-s(\S+)[^\n]*\n/-q((?:.|\n)+?(?=/-))}{}) {
            $q_num = 0;
            $auth{$a}->[$q_num] = $2;
            @s = split /,/,$1;
            for (@s) { (undef($s_nums{$_}) && $s_nums{$_} == 0) || ($s
+_nums{$_} += 1) }
            $subj{$_}->[$s_nums{$_}] = $2 for @s;
        }
    }
}
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