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Try with Dropbox (if you are using it) and set that folder (Vault) to sync offline. I use iCloud mostly to sync the computer settings, share amongst family members, but not for something which I need access locally such as the Obsidian/Markdown files. It works so far. I have over 5 or more Vaults (folders) managed by Obsidian via Dropbox.

The plugin "Remote Sync" works well too . It supports S3 , Drop box and many other cloud targets

iOS18 will bring "keep this always local" option for iCloud files

There's a setting to debug the starting time. It's interesting to find out the culprit (often a specific plugin)

If you are on a Mac, you have to disable in sys prefs iCloud “Optimize Mac Storage”.

Your files should no longer be removed.

Obsidian Sync is great, was worried you were describing it for a sec there