since the last update to Obsidian, all my files have completely disappeared. At first I wasn’t worried, thinking that they’d be in Time Machine - but they’re not. In every single back up as far back as I went there was a folder named Obsidian but it was empty.
I searched for files that are dot md but there’s nothing. I’m wary of using it now. How can I ensure that it backs up in Time Machine in the future?
It would help to periodically check that Time Machine is backing up the files you think it is. I would check it now to see if it is backing up my other, non Obsidian files as expected. If it isn’t, I would check its setup to see if it includes what it should. If the setup is correct, I would look for information about troubleshooting Time Machine.
Where is the Obsidian folder? Is that the name of your vault? Is it the app folder you have to use when storing vaults in iCloud on iOS? Something else?
If the vault was stored in iCloud, perhaps you forgot to set the folder to “Keep Downloaded”? That shouldn’t make files disappear from Finder, but in the case of files disappearing, perhaps it could prevent Time Machine from backing them up properly? (I would hope Time Machine behaves better than that but I don’t know.) Anyway, you should be able to log in to iCloud online and recover your files if they were deleted less than 30 days ago.
If the Obsidian folder is the one where the app is installed, updating the app will delete your files. If that is the case, I’m not sure if that explains the Time Machine situation (I don’t think it would even have to a folder). Anyway, never store your files there.
I hope you are able to find your files!
Thank you for your thoughts.
I don’t use iCloud - everything is on my laptop - and backed up using Time Machine - everything except Obsidian anyway. 
Looking at the back ups = all of my ther files appear to be there.
The app is in Applications, and the vault folder in in documents. and I’ve never encountered any problems with previous updates deleting notes.
I have given up finding anything form the past, and now would just like to have more confidence in Time Machine.
Thank you again.
I’m sorry to hear that. In Obsidian may be able to recover recently-changed files from Settings > File Recovery (unfortunately by searching each name individually). If you have any kind of sync setup, that may have its own (probably 30 day) recovery system.