I wouldn't use a skill challenge. This sound like more a job for old-school let the players solve it by creative thinking play. For a case like this I usually have a couple of solutions in mind, but expect that the players will come up with something workable that I didn't think of. As an example:
Scenario:
The PCs are looking for a particular book in the library of an abandoned building. It will take an hour of searching to find the needed title and the room is infested with bees. Anyone in the room will take 1 hp damage per round, and activities such as spells require a check to succeed due to distraction.
Approaches (some better and more serious than others):
Area effect damage spells will certainly kill the bees but will probably destroy the whole library.
Block the windows and build a smoky fire by the door to quiet the bees.
Plug up any gaps in the fighter's plate armor and let him go in and carry the hives out.
Have the monk run in, whack each hive with a stick, and lead the bees a wild goose chase.
As above, but use the NPC torchbearer.
Summon something impervious to the bees (like an elemental) to take care of them.
Search the library from outside via scrying then go straight to the needed title.
I definitely enjoy this type of play more than straight skill checks.
Yet this is EXACTLY the sort of scenario that an SC will produce better results for. As the PCs attempt various tasks they will narrate what they attempt to do, the GM will decide whether it can work or not, if it requires a skill check of some sort, if success or failure produces some sort of advantages or disadvantages or some kind of loss, etc. The SC framework then tells you how much success you need before the task is finished, whereas with the old 'shoot from the hip' method its anyone's guess when all the bugs are sufficiently run out of the library, the DM just calls the scenario when he feels like its enough, its arbitrary.
Nor does the SC solution void narrative, if the characters were to simply fill the room with oil and burn it all, well, they failed, obviously, if their goal was to save books. Likewise if they're willing to seal the whole room successfully and then expend a Stinking Cloud spell (a daily resource) maybe that's enough to succeed completely, though it depends on the weight (IE complexity) given to the encounter.
Now, we said earlier "don't use an SC for this" on the basis of its narrative weight as an encounter, but the key difference in your proposed scenario is there seems to be some sort of significant action going on, saving books. That might constitute a fairly major plot point.
I'll just add one thing here. You can 'reframe' challenges in many cases. Instead of a challenge that involves a single room, make the challenge more broad, like "get through the maze of rooms without taking damage or alerting the dungeon's inhabitants" and make the whole thing a single SC. Then the bug room turns into just one or two skill checks. This ability to 'zoom in and out' or compose several things into a single scene is a nice 4e feature of the SC system.
Think of it like an action movie scenario. In the first Indiana Jones movie they didn't show every single square inch of the temple scene. The party moved through various chambers and corridors, exploring as they went, presumably. Each interesting highlight, the various traps, the chamber of the idol, the rolling boulder trap, etc could each be simply one check in the process of a long SC. I'd also note the interesting results. Obviously Indy FAILED the SC, but this wasn't represented by death, instead it created a plot twist, his rival had time to appear on the scene and steal the treasure. I would then presume that the escape sequence was another SC or maybe a combat encounter.
