Not necessarily. It depends on what you still have. Assuming you had HBC version 1.0.8 (the latest), it is not lost during the update. And you can use that as a starting point.
Now...the update DID stub your cIOS'es. At the very least, you need to reinstall Waninkoko's 249 (preferably the same one you had before). It may be needed to use Any Title deleter (or dop-mii, or MMM) to delete IOS249 first (the official IOS249 is a stub: it exists and has a high version number, but it doesn't have any code).