I have used the cache cleanup tools extensively during performance testing and never had any corruption issues at all. I also have never needed to synchronize after running a cleanup. In my experience the cache will "auto clear" for simple, recent operations.
For example, if you create a new workspace, add several thousand objects, and then either delete the workspace, or delete all the objects in the workspace plus all the frames (events) related to that workspace, the recently added objects will automatically be cleared out of the cache. You can see this by watching the cache size after each operation.
The cleanup tools seem to be more necessary for things that have been left there for a long time or accessed by multiple workspaces. Keep in mind that the cleanup tools will NOT remove any object still listed in any of the workspaces or referenced by any frame (previous event). This means you are really just removing earlier iterations or versions no longer accessible by an earlier frame.
I am not a big fan of creating new caches primarily because I have many different workspaces containing many different objects that are either new and temporary (sketches, udfs, etc.) or contain modified, non-checked out objects that are not eligible for upload. Creating a new cache means I have to go through all those workspaces and do something with all these temporary objects, and checking in may not be an option.
I would say the vast majority of our users have NEVER recreated their cache in almost 2 years of operation. I've had my cache grow to well over 16 GB with no issue whatsoever.
(WC9.1 M050 + WF5 M120)