I did this quite a bit in the Spring. If you are staying that the same hotel, it will only count as one stay in terms of VIP bonuses and qualification. This is a drawback that currently has me switching back and forth between hotels.
What happens is somewhat hotel dependent. But make sure you are booking the same room type each night otherwise you definitely have to change rooms. Sometimes you can talk with the desk clerk about it at check-in. Sometimes they have no clue what you are talking about.
Smart packing can make the room switch easy as can be. One poster referred to it as packing in "layers" and that's a pretty good description of what I do. I switch hotels every night so I pack two nights at a time. I've got cheapo $10 Men's Warehouse garment bags which each hold 2 days clothing (hanging), 2 days of workout clothing and socks, shoes/flops, etc (in zipped pockets). Only one of the garment bags comes into each hotel (the others live in my trunk).
So when I check-in I only bring in three things: my laptop bag, one garment bag, and my dop kit/lysol wipes (wipes are vital in flu season) bag. Packing up in the morning is no problem and with a little extra effort all my stuff can make it back to the car in one trip.
The best part of this packing scheme is that if I'm in a hotel with a ... bug problem, I can drop "that" pack's contents at a full service laundromat in the morning, trash the cheapo bag, dump the dop kit, and head to Walmart/Target for new dop kit/contents. By check-in time, I'm whole again. Fortunately I've never had go that route but $50 and an extra hour of my life seems a small price to pay to avoid a costly eradication of bed bugs at home. In fact, when I pleasure travel with my spouse we still use this method.
Frankly with Express check-out/check-in I hardly notice that my reservations are split. To drop my keys on the way out, pick them up on the way in, and disinfect the remote and door knobs again takes maybe 15 minutes.