Sad to see old series like this disappearing over something as rudimentary as a copyright issue.. I'd be happy to help with that sound-replacing thing too if it becomes a community-involving effort. I've used Sothink SWF Compiler a bit in the past, but not sure that's any better than the one mentioned. Hope there's a way though.
As for old submissions going down, IMO it'd be great if we could have a system similar to YT in that content pages don't go down along with the submissions, just the infringing content itself, and an error message is shown in its place. Description, reviews, and all that information could remain even if the file itself is temporarily taken down (and the submission removed from the user profile), and review, voting etc functionality for that submission is simply locked until further notice. The error pages that we have now provide very little information as to what used to exist for each particular ID. Even with just the description and comments, a bit of the cultural heritage would be preserved, and people could re-visit those pages and remember.