I have created a new sync store (main-change-store), and in it I ticked the Inbox to be synced:
I thought the syncing would start by itself, but I guess I remember this wrongly, because even a day later the info still says “Not yet synchronized. Upload database”. (See screenshot above.)
How do I initiated uploading the Inbox database? I didn’t find a Menu item for this.
Any help is appreciated! 
This has been discussed many times… if you have a sync issue, the first things you look at are DEVONthink’s Window > Log.
Thanks. I have quite a few missing files like this:
I get these quite a bit when DEVONthink get out of sync with the filesystem (with Index folders like FileMe) – very annoying.
Now I have moved them to the Trash – and DEVONthink now started to upload the Inbox by itself.
Thanks for the hint with the log!
These files are Indexed or imported?
Indexed. I’d say nearly all my out-of-sync troubles come from Indexed Folders…
Another question about the syncing: Now the Inbox is synced, but I get these “Left-to-upload-items” messages:
How do I find out which items are left to be uploaded?
No surprise there.
I don’t have a magic “do this” as I’m not sitting at your computer. And I don’t have much experience with these sorts of sync issues, maybe because I have few to no indexed files that I sync.
That being said, there is lot already written in posts here and documented. No need to repeat here the admonitions about indexing already written about in the “In and Out” and “Troubleshooting” sections of the DEVONthink Manual. Also search this forum for “left to be uploaded” for info which may help. As a starting point, please re-read now that you have some first hand experience.
Edit: If not done already, do a “Verify and Repair” and “Update Items” on the database(s). Also “Re-build” may help and is not destructive to the database. More info on these features in the DEVONthink Manual. And, if the indexed files are in Dropbox or some other cloud-synced folder, maybe they are really missing from your computer as the sync-service “optimized” them off your machine? Check settings on the sync service to “keep files downloaded” or whatever nomenclature is used. Dropbox’s preference setting is called “Available Offline”.
