I followed your advice. I have narrowed my problem down to the comparison part of my code here: 
foreach (@contentsOfDataBase){
  chomp ($_);
  print "$_";
  @inDirectoryNotInDataBase = grep {!"$_"} @contentsOfDirectory;
  print "@inDirectoryNotInDataBase", "\n";
}

foreach (@copyOfContentsOfDirectory){
  print "$_";
  @pdfNoMatchingDirectory = grep (!$_, @contentsOfDataBase);
  print "@pdfNoMatchingDirectory", "\n";
  
}

[download]
They're nearly identical so it is the same problem in both. I changed the structure of the grep function to see if that would fix it. It didn't. The problem specifically lies in the grep line itself. This is how I understand that block to work. 
foreach (@contentsOfDataBase){
  chomp ($_);
  print "$_";
  @inDirectoryNotInDataBase = grep {!"$_"} @contentsOfDirectory;
  print "@inDirectoryNotInDataBase", "\n";
}

foreach (@copyOfContentsOfDirectory){
  print "$_";
  @pdfNoMatchingDirectory = grep (!$_, @contentsOfDataBase);#for curre
+nt element in @copyOfContentsOfDirectory find all elements of @conten
+tsOfDataBase that are not a match
  print "@pdfNoMatchingDirectory", "\n";
  
}

[download]

In reply to Re^3: Question of scope and syntax by Hellhound4
in thread Question of scope and syntax by Hellhound4

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