The GUIDs are initialized, stored and handled by Bios. So, it is possible that an AMT device gets null or invalid GUID but AMT will detect it as invalid and won't use it.
1) Will the system recover or re-generate the GUID at some point?
No. It is a bios issue and we can't do anything here
2) By saying AMT will not use it, do you mean the system is now incapable of provisioning (it should be in factory state at this point)?
It could be in the factory mode or in SMB mode if you put it in that way.
I have a simular problem...
I have about 20 computers reporting in my LANDesk Database with a AMT GUID of 00000000-0000-0000-0000-000000000001. Is there a way to reset this value?