Not sure how you effectively use Labels and Flags

I’m not really sure how you effectively use labels and flags to either search to say a TODO label or sort by that through the DB or say sort the whole DB by flags (used to saying sort at the top level flags and all flagged items would be the first items in the entire list of the DB).

Figured it out. You use the >tools/search< command from the menu.

Whenever I apply a flag or a label to an item in an indexed folder, they do not stick; the next time I open DT, the flags and labels have disappeared. Is there any way to make them persist, or is this behavior a function of the files not actually being in the database?

There is no known issue with flagging or labeling indexed files in DEVONthink.
Where are the files indexed from?

It is the directory that indexes the Bookends attachments in iCloud Drive. It is the only folder I have not imported into DT.

Is the metadata disappearing from files you are actively working on in Bookends?

No. The anomaly also happens if I close DT and open it in another computer: All but one of the files has lost the label and/or flag I had assigned it previously.

In DEVONthink’s Preferences > Sync, Control-click the sync location and choose Show Info. What options are enabled?

Everything is checked, except for “Verify uploaded items."

Hold the Option key and choose Help > Report bug to start a support ticket.

Fine; but to whom should the message be addressed?

“Report Bug” populates a new message on my email app, but there is no addressee.

What email application are you using?

Airmail.

Just a note: Airmail is a very poor choice for inter-application communication. You may want to consider this.

Send the ticket to support@devontechnologies.com

In the Finder, press Command-Shift-G and paste: ~/Library/Application Support/DEVONthink 3. When you respond to this ticket, attach the Console.log as well as the Sync.log from the Cloudy folder.