Does this mean the patch took?
Your saves don't automatically disappear when you install the patch, but you should probably not try to play them. Even if this works initially, you may encounter game-breaking bugs. For example, imagine not being able to finish the game due to a bug that makes the final boss invulnerable.
However, having replayed Bloodlines a few times, I can testify that replaying an episode is much, much faster than playing it for the first time. So, just play till the sewers part, it really won't take you too long.