Any disk utility you try would have to be available on a live CD, which you would boot the VM from. The hdd should be mounted in the same VM, and I would choose the 60GB hacked version of the drive, ideally hacked from clean backup copy - not applied to a drive that had already been tampered with.
I can't recommend any disk utilities, you'll have to do your own searches on that. You'd be looking for a super chkdsk, ideally Win7 compatible (though I don't think you've actually said what the guest is), or something even more low level.
The big puzzle for me is why you saw empty partitions - enlarging a disk does not create empty partitions. It's like some kind of disk repair had already been applied - no harm in that provided you made a backup first in case it made things worse.