Comment by C4K3
At the very least they should have excluded any chats with disappearing messages enabled from being included in backups.
With disappearing messages off it was already reasonable to assume that a compromise of a counterparty's phone would result in exposure of all previous messages, so enabling backups wouldn't expose you to new risk.
That would cater to those who want to keep their chat history forever without exposing those with disappearing messages enabled to new risk.