Those "Dangling documents" are indeed ghost documents that have been removed from their original location without first removing any and all reload tasks and/or document CALs. This way, QMC indicates that it has task/CAL assignments for documents that do not exist anymore. The ghost documents end up in the Document tree root (if you don't have a publisher license) and have their names all in CAPITALS.
How to get rid of them? Free the assigned CALs and/or remove all linked task definitions (Reload tab). The easiest wxay to do this is to recreate those documents (0-length placeholders will do just fine) in their original locations, open the QMC and (if they moved from the root to their proper location) unassign CALs and clear Reload settings/task definitions). After these have been completed, drop the placeholder documents. They will not reappear...