OK, it looks like this might be a problem with the driver code rather than with the SDK and it should be possible to fix it in /indi-3rdparty/indi-qhy/qhy_ccd.cpp.

One problem which the QHY support pointed out to me and which I already confirmed in my smoke test is that after a read mode change the camera needs to be re-initialized by calling InitQHYCCD(). In my test I was able switch the camera to 47M mode and acquire the larger frames. The other problem I see is that in order to pass it's sanity check on the user defined resolution the code may need to update the effective frame area (GetQHYCCDEffectiveArea()) after the read mode change and camera re-init instead of doing this first.