Hmm. I turned off sync for the relevant database on the other Mac (MacBook) syncing.
On my main Mac, I ran File > Synchronize Database (just to be sure things were in sync). Then in DT Settings, I tried to clean the iCloud (Legacy) store, but got a dialog box:
The local databases contain not yet downloaded files.
Do you want to remove all sync data from the sync store anyway?
I cancelled the operation, ran the sync again, and this time in Settings I first clicked off the relevant database in the iCloud (Legacy) database pane, and tried cleaning the iCloud location again. I got the same message.
A search in this forum led me to this post: Cleaning sync locations with "not yet downloaded files"
There, a search for item:pending located a file that couldn’t be downloaded; removing it from the database (and clearing the trash) fixed the sync block.
I tried that and it worked. But the puzzle for me is that there was just one pending item, and it was in another database—one being synced via Dropbox—not the database being synced via iCloud. Is there a reason the pending item in that other database in another store is blocking cleaning the iCloud store?