In order to synchronize copies of a virtual disk, a virtualization layer maintains a first record of file system blocks of a first copy of the virtual disk that are modified during an access session by a virtual machine using the first copy of the virtual disk. The file system blocks correspond to a file system of the virtual disk. During an attempt to synchronize the first copy with a second copy of the virtual disk, (i) a second record of file system blocks that are currently used by the file system is obtained from the guest operating system, and (ii) file system blocks in the first copy of the virtual disk that are present in both the first record and the second record are copied into the second copy of the virtual disk.