Most likely the bonus content will still come to see the light of day, keep in mind Disney is a business. You use the terminology vault I believe, in reference to the "Disney Vault" it's many classics seem to disappear into after a brief initial release. However, the "vault" is merely a business strategy used to- catch impulse buyers with it's "limited time only" promise and to keep the prices of merchandise high. With the sizable following the Clone Wars has, more likely than not we will see several of the arcs become direct to video releases or become bonus content on prequel trilogy releases to help boost sales. (come on anyone can argue that the movies are just fine all anyone wants, but I when I got to Walmart, Target, or Best Buy they always have WAY more prequel trilogy collection sets in stock than original trilogy/complete saga ones.) Anyway long story short stop worrying, we'll get to see what was developed from season 6, and hopefully the new series will be just as good.