while (<HANDLE>) is short for while (defined($_ = <HANDLE>)), which sets $_ but does not localize it. You can use a different variable explicitly: while (my $line = <HANDLE>) (the implied "defined" on the result of the assignment is still added), or, beginning in 5.10, you can lexicalize $_:

foreach (@blah) {
   do stuff with $_ from @blah
   {
      my $_;
      while (<HANDLE>) {
         do stuff with $_ read from the handle
      }
   }
   do stuff with $_ from @blah
}
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