"Now, when I exit Opera and restart it that listing is blank save..."
"I've tried creating a new folder, on /root, and set Opera to use that one but the listing is cleared on every exit. But again, the actual files aren't being deleted, they seem to be hidden to Opera."
Yes, this is absolutely fact!
Eventualy i ain't alone
@hassunaa When you reset your synced data, it is removed from the sync servers but should remain locally. However, like in any synchronization service, any change may replicated to any connected device, leading to data loss.