Depends. If the carto has been in there a week or two already, it's probably ready to be exchanged for a fresh one. If it's only been in there for a couple of days and you are going to be switching to a flavor similar (fruit to fruit, tobacco to tobacco, etc), you can just refill the tank with the next flavor.
If the next flavor is something not complimentary with the first, you will need to pull the carto out and start fresh. The first carto could possibly be saved for another time by taping the punched holes and putting the old condoms back on that came with the carto, if you saved them.
If changing to a new carto and the remaining
juice is looking dark, I dump whatever juice might be left. It has components that were not vaporized and have accumulated over time and likely has begun to lose good flavor. I run the empty tank under running water, and use a Q-tip to scrub the inside of the tank if it needs it.
Having a tank tool makes the whole process a lot easier, and also protects your end cap o-rings.