Nesting conditions will help you avoid retesting the same conditions, though you may have to look harder to see what branch you're following. I think I've kept all the logic from your main section.

    if ($macf == 0) {
      if ($syman == 0) {
        if($mac eq $oldMac)
          if ($sym eq $oldSym) {
            print "no changes\n";
          }
          else {
            print "SEction E updated\n";
          }
        }
        elsif ($sym ne $oldSym) {
          print "section C UPDATE\n";
        }
        else {
          print "section B UPDATE\n";
        }
      }
      elsif ($mac ne $oldMac) {
        print "MacSEction updated\n";
      }
      else {
         print "no changes to mac\n";
      }
    }
    elsif ($syman == 0) {
      if ($sym ne $oldSym) {
        print "syman update\n";
      }
      else {
        print "no changes to syman\n";
      }
    }
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