Yes, the sync issues in the stable version are the main reason for the new sync system in beta. “Stable” is a bit of a misnomer - it’s stable in that it doesn’t update as often, but there are bugs we’re working on fixing in beta.
One of the major changes is that items were referred to solely by ID, but then moving them to another document retains that ID (so that links/mirrors still work) and would mark the old ones as “moved”. But then moving items back and forth caused some strange bugs, sometimes it could only complete part of a move, and sometimes old moved items would pop back up in the old location. The new system refers to items by document+itemID and does moves in a much better way, so that should be fixed.
As Jerud said, the data can’t be lost because it doesn’t actually “delete” anything. It marks items as deleted or moved, and then they’re not shown. So the data is there but some bug may be causing it to not display.
The beta also caches to a folder when using the desktop app, so it’s much easier to back up that folder yourself, just in case anything happens.
The main goal of the new beta sync system is to be 100% correct with sync. I’m using the beta version myself and am trying to stress test it in every way I can think of, and it’s holding up. A lot of the remaining issues now are finding and repairing issues in documents that were caused by old bugs, like the latest update fixes items marked as “moved” incorrectly. I’m planning to focus 100% on sync stability until it’s perfect.