It is probably simpler to just slurp the entire file into an array and replace the while(<>) with an iteration over the array (untested code follows):

my @data = <>;
my $backup=$commandfile.".bak";             
foreach $com (keys %hashnew) { 
   $ARGV[0]="$backup";
   $^I=".bak";
   foreach (@data) {
     if ($hashnew{$com} == "all") {
        unless (/$hashnew{$com}/../\*\ Exit\ context\ \*/) {
             s/$com//g;
                          }
             }
     if (/$hashnew{$com}/../\*\ Exit\ context\ \*/) {
             s/$com//g;
                          }
             print;
            }          
    }
[download]

Of course if you actually explained to us what you want to do we might be able to come up with a better suggestion as it is not entirely clear from your code.

/J\