I've done this many times. I tend to use Megabonus or credit card certs as part of 3-day weekends where either a Thursday or Monday night is expensive (so I use the cert) and I pay the regular rate for the other 2 nights.

Only once has it ever happened where Night #1 (a one-night stay) included a full suite upgrade. I told the FD right then about the subsequent reservation, saying I'd rather stay in a lesser room than have a huge suite for one night and have to move. He looked in the system and confirmed then I could have it for a 3-night (I think) stay, but I realize that was a fortunate exception...