Systems and methods are disclosed that track a document within a file system using document identifier (DOCID) that is preserved during safe save operations. The DOCID can be a universally unique identifier (UUID). The DOCID can be generated on a local file system or generated during a synchronization process with a remote synchronization service. Applications can opt in to document tracking. The kernel of the operating system can monitor file system operations on a per-application and per-thread basis and determine when a processing thread is about to perform a safe save. When a sequence of file system operations indicates that a safe save is to be performed, the kernel can generate and store a tombstone record that includes the DOCID and other metadata of the tracked document and pass the DOCID and metadata to the newly saved document.