If a document is deleted from an indexed group (folder) then from that point forward DT ignores the document in the target Finder folder and will not synchronize it or display it in the group again. (Why this is “synchronization” isn’t obvious.)
Since DT will delete documents without warning, it is easy to do and not notice until long after the trash is emptied and the document long gone. The only recourse is to delete the indexed groups and reindex from Finder. This causes all replicants, links to annotations, etc., to be lost. A simple file deletion can lead to a big mess that is difficult to recover from.
So, why not have a command to force DT to re-index? Or why not make synchronization restore the links to the content of indexed groups from Finder? Or have a script or utility to compare DT indexed groups to the original Finder folders and note differences and missing documents?