Fix init complete when upgrading from partial

When upgrading from partial init to full init using vmi_init_complete* the old flags are taken from the vmi instance which has VMI_INIT_PARTIAL already set, therefore both VMI_INIT_PARTIAL and VMI_INIT_COMPLETE will be set on the new instance. Partial init only happen if that's the only flag set. Otherwise I think we can keep having both flags set, that would just indicate that the instance was upgraded from a partial init to complete.