Here's the loop with the grep you think is failing as you posted it:

      foreach my $filename(keys %Hash_filenames) {
     @{ $Hash_filematches{ $filename } } = grep( (/\/\Q$file_name\E#/i
+ && !/\.plf/), @{ $Hash_filenames{ $filename } });------>this grep se
+ems to be failing,
      }#for loop end
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There's no print statement.

%Hash_filenames has no keys: the last occurrence set it that way: my %Hash_filenames=();

There are two other foreach loops in your code: one looks nothing like this; the other says the grep worked.

I suspect you're getting very frustrated: your post which you almost immediately said to ignore followed by the double posting of this one rather bears that out. Friendly advice: take a break, collect your thoughts then come back to this code when you're feeling refreshed and ready to tackle it again. Been there, done that, know what I'm talking about. :-)