If your files are in iCloud, there’s a possibility that iCloud is one, if not the sole, culprit. iCloud is notorious for having synchronization problems. Check out Howard Oakley’s advice.
(Personally, my vaults are never on cloud services, residing in ~/Documents. My vaults used to be on iCloud, and these mysterious “missing files” issues were common. Since moving everything to Documents, the problem never occurs for me. I use Obsidian Sync, but there are other low-cost/no-cost optoins. See the Obsidian sub-Reddit for extensive discussions of options.)