Thanks for the info . What's strange is that "Deduplication" and "Store backups in separate files" are both listed as repository parameters at the same time - when really they are the negative of each other aren't they? Like - it's not possible to have both be enabled, or both be disabled, is it? It's like you haven't introduced a new feature, but just added another name for an existing one, greatly confusing people in the process.
I suspect "store backups as separate files" (aka no deduplication) would take up too much space. But I also find that global deduplication is risky, for the reliability reasons you've listed above. What I was hoping you were doing with this new feature, is to have per-VM deduplication, rather than global. That way if there is any corruption, then it would/should only affect a single VM, and I could just start backing up that VM from scatch again, rather than blowing everything away - which takes a long time to do for that inital backup (I can only start that on a Saturday afternoon).
To me, that's a great trade off between global dedup vs no dedup. I was really hoping this new feature would be "store VM backups seperately" with the option to still have deduplication on (on a per-VM basis).