Today on the community forums someone mentioned an issue where his VMs were not protected by vSphere HA after they had been migrated between clusters. After reading it I vague recalled this being a known issue. I dug up the KB and the work around is fairly simple:
- Disable HA on the cluster where the unprotected VM resides
- Enable HA on the cluster again
If you need to do a lot of migrations to a different cluster you can also temporarily disable HA, migrate all VMs and then enable it again. This leads to the same result as above, all VMs will be protected again. This is on the radar of our developers and they are working on fixing this in a future release.