First for the shove in the right direction: It sounds like you might be doing EDI X12 stuff. If so, search CPAN for relevant libraries. Chances are very good you are reinventing a wheel.

Now, these seem like a case where you likely can write some nice, elegant code. Not being familiar entirely with what you are doing, let's go over a quick example:

sub invalid_line {
    my ($line) = @_;
    ...
    return 1 if $invalid;
}

my @files;
# todo, get list of files

for my $file (@files) {
    open FILE '<', $file;
    if (scalar grep { invalid_line($_) }
               grep { $_ =~ /^$keyword/ }
               <FILE>
    ){
        # file is invalid
    } else {
        # file is valid
    }
    close FILE;
}
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