Unfortunately we know that migrating from HE to HE is not as simple as from physical to HE: https://bugzilla.redhat.com/show_bug.cgi?id=1240466#c21 In general the issue is that the DB backup form the old hosted-engine VM contains a lot of references to the previous hosted-engine env and you cannot simply remove/edit them from the engine since they are lock so you have to manually remove them from the DB which is quite risky/error prone.
This is a bit scaring. In case of issue with engine and trying to recover, it could also happen. What other way would you suggest for backing the engine VM and being sure to be able to restore it as it was without errors ? Have you ever tried to backup/restore from rsync ? If there are data in the DB written when you're performing it, do you think it can cause issues ? If ovirt-engine service is stopped, is that problem avoided ?
In the mean time I'd suggest, if feasible, to redeploy a new hosted-engine env and reattach there your storage domains and your hosts. This will imply a downtime.
Ok, I think I'll do that. A downtime isn't a problem right now, as I'm still at a pre-production step. (preparing it for production soon)