Looking at your scenario, wouldn't it be most straightforward to simply remove your Bonvoy number from the shorter stay so that it is blind? I don't know if you can do this beforehand to your reservation online or ask the hotel to do it at check in but surely if you can add a Bonvoy number at check in then you can also ask the hotel to remove one. Anyone?

Then you are left with two exactly concurrent, qualifying, reservations under your Bonvoy account which should post as two line items: both generating points and one generating the EQNs.