There is disclosed apparatus and a method of de-fragmenting file allocations on a disk comprising: determining what pages should be swapped among the various allocations made by the operating system (OS), the OS's file system mapping updated to reflect the swapped pages and a history of the original state prior to any update recorded by the engine, the swaps performed by manipulation of the engine's data structures and/or actually exchanging data on disk where OS visible data is read and written but the original state of each altered page is not directly recorded in the historic log, but instead, a record is additionally logged of the locations of the swapped data so that an image of the OS visible data can be reconstructed prior to time of the de-fragmentation by knowing what data to effectively re-swap and what OS mapping data to effectively restore. The apparatus and method may include the step of incorporating desired close proximity information of various OS visible pages into the algorithm executed by the engine that determines what is actually swapped, in order to reasonable maintain physical close proximity of data allocated by the OS but physically re-mapped by the engine.