When no Label filters are applied to your PRISMA 2020 flow diagram, any quarantined references in your Project are captured in the flow diagram (e.g. those quarantined via Duplicate Detection would be categorized under "Duplicate records removed").
However, once a Label filter is applied to your whole diagram, if your quarantined references were not labeled with that Label, they will not be counted in the flow diagram. To remedy this, all the quarantined references must be retroactively labeled.
This can be done by removing those references from the quarantine, labeling them, then quarantining them again.