A system for retroactively detecting malicious software on an end user system without performing expensive cross-referencing directly on the endpoint device. A client provides a server with information about files that are on it together with what it knows about these files. The server tracks this information and cross-references it against new intelligence it gathers on clean or malicious files. If a discrepancy is found (i.e., a file that had been called malicious, but that is actually benign or vice versa), the server informs the client, which in turn takes an appropriate action based on this information.