This distinction should be captured in the guide when DwC-DP is supported:
Please be aware that there are terms in the MolecularProtocol table that have information relevant for either the rawTotalReadCount (terms to capture relevant lab protocol steps/decisions) or the processedTotalReadCount (terms to capture bioinformatics pipeline settings, thresholds, chimera check etc.). I do not think this causes any conflict for keeping the IDs unique, but end-users should be guided to understand which terms support either of the read counts shared.
tdwg/dwc#649 (comment)
This distinction should be captured in the guide when DwC-DP is supported:
tdwg/dwc#649 (comment)