After a closer look, I notice you have ($newbase = $base) on both conditions of your tertiary. My first thought was instead, my $newbase = $base;.

But, you only need $newbase if $base matches the pattern. Further, you stop using $base; you may as well make changes to it rather than $newbase.

So, perhaps this:

...
for ( @found ) {
   my ($base,$dir)     =  (basename($_),dirname($_));
   next unless $base   =~ /$pat/;
   defined $opts{n}    ?  $base =~ s/$pat/$rep/ 
                       :  $base =~ s/$pat/$rep/g;     
   my $newname         =  File::Spec->catfile($dir,$base); 

   if (-e $newname) {
      warn("can't rename $_ to $newname: $newname already exists\n");
   } else {
      rename($_,$newname) or warn "can't rename $_ to $newname:$!\n";
   }
}
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