The usual reason for corrupting the first few bytes of a binary file is someone tried to edit it with Notepad or suchlike.
p.s. I think I'm going to lock this topic. The original posts are from 2014 (7 years old), and contain information that's dangerously out of date, for example that VDIs are aligned on 4K boundaries (not any more - it's became 1MB not long after).
In summary, if you have a stand alone VDI with a corrupted header then use CloneVDI to fix it - adding this as an automated feature to CloneVDI is something else that happened years ago. If you have a corrupted snapshot then I suggest prayer, and why the hell were you using snapshots after all the advice telling you not to?