Since updating to Obsidian 1.13.5, and still on 1.13.6, I’m experiencing a reproducible issue where entire nested folders suddenly disappear from Obsidian, even though they remain present on disk.
The issue persists with Restricted Mode enabled, so it does not appear to be caused by a community plugin.
There is also an important clue suggesting that this may involve the interaction between Obsidian and iCloud Drive: if I copy the same vault/files to a completely local location and open that copy as a vault, I have so far been unable to reproduce the problem.
What happens
My main vault is stored in iCloud Drive, with the entire vault explicitly set to “Keep Downloaded” / “Always Keep on This Device”.
The issue originally became apparent when moving notes from a root-level Inbox folder into more deeply nested folders, although I have since experienced similar disappearing-folder behavior while simply working with files as well.
When the issue occurs:
- Obsidian freezes or becomes unresponsive for a few seconds.
- An entire higher-level folder disappears from Obsidian’s native File Explorer, together with all of its nested folders and notes.
- The files and folders are still present in Finder/iCloud Drive and have not actually been deleted.
- The missing notes can no longer be found through Obsidian search either, as if Obsidian has completely stopped recognizing that portion of the vault.
- Restarting Obsidian makes the folder and its files appear again.
- After restarting, Obsidian appears to re-index a substantial part, or possibly all, of the vault.
The issue seems to affect certain nested folders, while root-level folders appear less affected.
Reproduction / normal workflow
My normal workflow is:
- Create notes inside a root-level
Inboxfolder. - Later move them into their final location within a relatively deeply nested PARA folder structure.
A typical trigger is moving a file from the Inbox into a folder located several levels deep.
The issue occurs when using:
- Obsidian’s native Move file to… command.
- Drag and drop inside Obsidian’s native File Explorer.
Most importantly, I can reproduce the problem with:
- Restricted Mode enabled
- Community plugins disabled
- Obsidian’s native File Explorer
- Obsidian’s native Move file to… command
I have also seen the disappearing-folder behavior simply while using files, without necessarily moving them immediately beforehand.
Files are not actually deleted
This is probably the most unusual aspect of the issue.
When a folder disappears completely inside Obsidian, I can open Finder and confirm that:
- the folder still exists;
- its nested folders still exist;
- the Markdown files are still present.
The problem therefore appears to be that Obsidian temporarily loses awareness of part of the vault rather than actually deleting anything from disk.
Restarting Obsidian causes those files and folders to be detected again.
Possible iCloud involvement
My main vault is located in iCloud Drive.
However, the entire vault is explicitly configured with “Keep Downloaded” / “Always Keep on This Device”, so all of its files should remain locally available rather than being dynamically offloaded by iCloud.
As a troubleshooting step, I copied the same vault/files to a purely local directory outside iCloud Drive and opened that copy as an Obsidian vault.
So far, I have not been able to reproduce the issue in the local copy.
This makes me suspect that there may be some interaction between Obsidian’s filesystem watching/indexing and macOS/iCloud Drive (possibly File Provider events), even when all files are configured to remain downloaded locally.
Of course, this does not necessarily mean iCloud itself is at fault, but the difference between the iCloud-hosted vault and the local copy seems significant.
Sandbox Vault
I have also not been able to reproduce the issue in the Sandbox Vault.
My main vault is considerably larger and has a deeper folder hierarchy, so there may be some combination of:
- vault size;
- folder depth;
- filesystem events;
- and iCloud/File Provider behavior
that does not occur in the Sandbox Vault.
Environment
Obsidian version: 1.13.5 / 1.13.6
Installer version: 1.12.7
Operating system: macOS / Darwin 25.6.0
Architecture: ARM64
Language: Italian
Catalyst license: Insider
Insider builds: enabled
Vault location: iCloud Drive
iCloud setting: Keep Downloaded / Always Keep on This Device
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