It is true that the saved games have been invalidated with the last patch, just like how they were with the first. But, since there seems to be about 3-4ish weeks between patches (so far) and the last was 6 days ago, there should be enough time to start again and finish the Bonus campaign.
Even though the save games are not recoverable, there are some things that can be done to soften the blow when the saves are lost: