You don't need to re-encrypt the entire vault, just whatever you're using the PBKDF2-derived key to hide. In most situations, you'd use it to encrypt another, separate key. In that case, it can be readily upgraded at any time, including during login.

Conceptually, it's not very different from how password hashes are updated, just that you need to re-wrap some other key as well simultaneously. Since the rest of the vault is unaffected, it's OK if the transaction fails: the old parameters will work with the old wrapped key, so all you need to do is ensure that the transaction is atomic. (Usually don't even have to do anything to ensure that if you just use the same database table/object.)