You are punished for changing the game time (no matter how much, it seems), but not the system time. Here's what happens:
If you change the time on your 3DS system, Animal Crossing seems to simply think that's the time it is now. Trees grow, events change, the only "bad" things that happen would have happened with the flow of time. Even going back in time via this method seems to work okay, even when going to a day previously played.
If you change the game time, using the option at the main menu of Animal Crossing, you will randomly trip for a while after changing the clock. The duration of tripping seems to last longer than the current play session, possibly the full day? But it eventually goes away. If, however, you were to change the game time this way before every play session you would trip randomly every single session, which is highly frustrating.
Also note that going backwards in time will spoil any turnips you had, since the game knows you went backwards, while it doesn't know you went forwards if you go by the system clock.
tl;dr: Change your 3DS's system time to time travel, do not mess with the in-game clock regularly or will will randomly trip.
Based on past animal crossing games and judging from a week's worth of experience, items will persist forever when dropped until picked up, and they will be moved to the "lost and found" (does this exist in AC:NL? I haven't seen one yet) as soon as an event or new house needs to occupy the space the item took. In the original AC I left items all over several acres of land and they were only removed when (oops) an event cleared the acre.
I haven't noticed any dropped items disappearing so far. Note that buried fossils and gyroids are an exception to this rule; naturally placed buried items will be removed the next day.
Best Answer
In Animal Crossing: New Leaf, the game stores 16 different non-residing villager characters. These stored characters will show up in the shopping district area, stores, etc. Usually, these stored characters are all past residents of your own town, but occasionally you can pick up the character information from another town you've connected to. Rarely, they can be characters randomly chosen to wander your game.
Will these wandering animals ever leave? So like I said, the game stores 16 characters. 16 unique characters. This means you can rotate her out of the stored characters by allowing current villagers to move, eventually bumping out the unwanted character.
I've used this technique to get back one of my favorite villagers, who accidently moved out. Villagers that are on this 16 character list will not move back into your town. I bumped him out of the 16 (basically out of the game's memory of the character) so I could adopt him from a friend's town when he was in boxes.
The game has this weird system to make the in-game relationships more realistic. How weird would it be if a villager moved out your best friend and moved back in 3 days later, introducing themselves like they've never met you?