Could still be same issue. Check firmware
If the NVMe SSDs being utilized were being accessed by the QM2 card in the same way they are intended to be by the Drive Manufacturers, the firmware on the NVMe SSDs should not make a difference, since no matter what, those drives always have to support the base specification.
I could understand if I was doing something cutting-edge or unusual, such as NVMe-oF (NVMe over Fabrics) or over-PCIe, RDMA, etc., but as far as I am aware, what the QM2 card is doing is a super-simple, standard read/write operation that should be universal across all NVMe SSDs in that form factor – assuming the QM2 card is using the commands defined in the NVMe base specification.
If it isn’t… and instead is doing some kind of direct access of the drives in a manufacturer-specific, drive-model-specific, outside-the-base-specification-commands way, this could explain why firmware differences (which could easily result in changes to those non-standard paths on a model-by-model, update-by-update basis) would be an issue.
I’m not sure why QNAP would do that, though. It’s so much simpler to just follow the base specification, and then they would also have 100% compatibility with all NVMe drives, with no need to worry about different models or down-the-road firmware updates breaking what they set up at the time of developing the QM2 board.
But even if that was the case – if QNAP did that at some point in the past for some marginal performance gains – and they wanted to roll that back now, switching to only using the standard NVMe specification, I suspect they could do it with a simple Firmware update to the QM2 card.