As long as the DEVONthink database is in a folder “back-up-able” by BackBlaze, it will back up the database.
But as it says in the “DEVONthink Manual”, indexing files into DEVONthink “Creates links to files outside the database.”
Files not in the database won’t be in the database to be backed-up inside the database. Files *imported" to the database will be backed up.
See in the “DEVONthink Manual” (and in the app’s Help) Chapter “IN & OUT”, section “IMPORTING & INDEXING”, page 53 of the 3.9.7 version.
While there also see page 19 “A WORD ABOUT BACKUPS” with some good advice. Hopefully you also have another more complete system backup, say with macOS’s TimeMachine from which to restore the missing files back into their previous locations.
I have downloaded various snapshots of the database over the past few weeks and it is curious. Some have the groups in there and some don’t.
I will interrogate this more thoroughly.
Of course, as the files are indexed, I haven’t lost any files, and I can easily re-index, but I am trying to avoid that as I will lose all my existing DEVONthink item links.
One workaround might be to set the path via AppleScript, e.g.
tell application id "DNtp"
if (count of selected records) is 1 then
set path of selected record 1 to "~/Library/Mobile Documents/com~apple~CloudDocs/Documents/Household"
end if
end tell