It's not my idea but I was asked by several clients and I'm not the only VAR with that problem (or client).
It's all explained here : http://forums.autodesk.com/t5/Autodesk-Vault/Find-Files-in-my-Workspace-that-are-not-in-the-Vault/m-...
The idea is to easilly find in the workspace (I mean local workspace as managed by vault IPJ) the files that are not yet checked in in order to clean or check in those files.
It could be integrated in the synchronisation tool as an option like "detect non vault files in the workspace" and the ability to choose what to do with those files.