I also have this issue.
If I create a new item in Obsidian (stored on iCloud, using only that for sync), and then delete that item in Obsidian, DT still shows the item. The DT log shows it as a “Missing File.” The vault is only indexed in a single database.
As Korm suggested, I do have some community plugins. Disabling those, restarting both Obsidian and DT3, did not resolve the issue.