One of my tablemates on a cruise several years ago on another cruise line was doing back-to-back cruises. She had evidently booked a guarantee, as she didn't know until maybe the second-last day of the first cruise if she had the same cabin, so she had to be mentally prepared to check out, disembark, then wait to get back on again. However, as it turned out, she didn't have to do that, and was able to relax on the changeover day.
I would hope the cruise line wouldn't make you check out and recheck in, but you may want to ask to be sure. Post-9/11, they may have some new security rules.