I'm using the latest version of W3TC (recently upgraded) and I don't use its database caching because I'm using HyperDB instead.
I noticed that after the upgrade, any time I clear the cache, the plugin deletes HyperDB's version of db.php. This may be because this time I actually disabled database caching in W3TC's configs (before, I kept it enabled and just replaced db.php with HyperDB's but since the newest version displays the annoying red warning now that can't be dismissed, I ended up unchecking db caching).
There's no reason clearing the cache should delete db.php. Enabling or disabling db caching should do the appropriate db.php mods, but not just clearing the cache. W3TC works fine with HyperDB if db caching is disabled, but this makes it impossible to do. Please consider not removing db.php upon cache clearing.
Alternatively, I feel like there's only a little bit to support HyperDB with all its benefits (such as being able to use master-slave DBs and achieving high availability). Perhaps W3TC can be finally pushed over the finish line?