The Cloud API number does not replace the QR number. Both live on the same workspace at the same time, and an agent working the queue does not need to know or care which connection a thread arrived on.
That pairing is the point. A WhatsApp Cloud API number cannot be linked as a device, so a tool built only on QR cannot offer compliant broadcast; a tool built only on the Cloud API cannot reach WhatsApp groups, and charges a per-conversation fee on top of its subscription. Running both is how Indian businesses actually use WhatsApp.
Comsky Chat will not send a broadcast over the QR connection, by design. Bulk sending from a linked device is the fastest way to get a number banned.