I just released an update to the beta which should fix a lot of the sync problems (as I mentioned above in https://forum.legendapp.com/d/906-new-sync-system/34), and it may load faster for some of you.
It’s not possible for any update to delete anything - there’s not even code anywhere for deleting items or documents. Deleting items only marks them as deleted, but all the data remains, and they would be in the Deleted view. Similarly deleting documents only marks them as deleted and then they’d be in the Trash. So I think documents disappearing would most likely have been a bug in the stable sync system that didn’t save it properly, or it’s a bug in the beta where it’s not loading as expected and just ignoring it. But if you’ve seen in on more than one instance before it is still in the database.
If the beta is not showing any particular document that is appearing on stable please tell me the name of it so I can investigate your account in the backend and see what about the document would make it fail to load in the beta. I have been stress testing this pretty hard and haven’t been able to find any ways to break the sync, but it’s possible that some old bug from long ago put a document into a state that the beta is having trouble loading.
The bug with new My First Documents being added is still on my todo list. I saw it happening a while ago when signing into an account with a single encrypted document, but I thought I’d fixed it. I’ll keep looking into it.
Also if you’re concerned about your data I’d recommend doing a manual backup just to be safe. Using the beta in the app now saves to .json files so you can keep the folder backed up to Dropbox/Drive/git or whatever backup method you use. But for now it’s probably better to run it in an incognito window for testing.