Missing manifest error

Welcome @LightCreator

And yes, this is a matter of concern as it’s issues with the transactional sync data.

In DEVONthink’s Preferences > Sync, select the sync location, Control-click the database in the database’s list on the right, hold the Option key, and choose Verify Database Thoroughly. Results will be reported in Window > Log.

If the Log window shows errors, Control-click the database in the sync location, and choose Clean Database. After the clean has been reported successfully in the Log window, enable it for syncing again. Repeat with other databases, as needed.

I would ask if you ​need ​to use a remote sync option like CloudKit. There is a forum post discussing the options and considerations of the available sync methods.: Sync Types Explained​