This doesn't apply to the target attribute, but here's a workaround to combat losing any custom css styling after reentering the wizard - if anyone is interested.
I've been designating custom styles (like CSS3 styles or <li> class styles) to a separate stylesheet, placed below the menu.css that MenuWriter generates. You can re-enter the wizard to make edits, and unless you make major menu structure changes, the custom style sheet should still target your menu's tags. If anything goes wonky its usually not hard to pinpoint the problem selector and fix accordingly.
Sort of adapted this method from Dan Cederholm's book, ‘Handcrafted CSS’ in which he adds an enrichment css file to the bottom of the style sheet stack to utilize the cascade effect and server up CSS3 styles to modern browsers. The beauty is in the fact that the MW wizard won't touch this file and alter it on you.