Did you ever exclude any items from searching, see Info inspector? Or anything in the trash?
I don’t recall ever using that option in the Inspector, I think I actually just discovered this option now…
I’ve emptied the trash and synced. I get the same result:
Also, any idea on why the sync icon would not stay darkened after sync is complete? Is it related maybe?
Please…
Select the Help > DEVONthink 3 Help > Documentation > Appendix > Hidden Preferences.
- If you’re on macOS Big Sur or earlier, click the On link for the SyncDebugLog.
- If you’re on macOS Monterey or later, Control-click the On link for SyncDebugLog. Then paste into the address bar in Safari, okaying opening DEVONthink.
Quit and relaunch DEVONthink and manually initiate some syncing. Then hold the Option key and choose Help > Report bug to start a support ticket and we can look at the logs and info.
Done.
BTW, “Report bug” needs the option key, took me a while 
Also, I noticed the log file goes a bit back, so I should tell you that this morning I’ve moved everything server related to a non-admin user (still using the same domain name, nginx and WebDAVNav, although the storage location path for the sync store is slightly different). Just in case you notice things aren’t exactly the same between yesterday and today.
Thanks a lot.
Indeed! As I instructed… Then hold the Option key and choose Help > Report bug 
Sorry, my bad. I’ve been reading through WebDAV configuration steps all day…
Sounds dreadful
You’re not even close