A method for converting a physical file system to a virtual file system of a virtual machine. The method includes initiating a new incremental physical to virtual conversion process, and analyzing a history of a plurality of prior incremental conversions to determine whether there exists at least one prior incremental conversion that failed. Upon determination that a prior failed incremental conversion occurred, the method further includes determining a correct chronological order of the plurality of prior incremental conversions, and determining an original failure point and any subsequent failure points. The prior incremental conversions are re-applied from each of said original failure point and said subsequent failure points in the correct chronological order with the most recent incremental conversion re-applied last.