Sudden Changes in Behavior, May be Dangerous?

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I just received my precious little Kiki five weeks ago. She was litterbox trained, save the few pellets she leaves around her cage. I was told that this is a normal thing for rabbits to do by the old owner but have read contry.Her cage is a large dog kennel that she came in, so there is plenty of room for her to jump around. Suddenly a few days ago, her litter habits shifted. I was out of the room longer than usual, actually a couple of hours. She has a really large pen I wrap around her cage so she can be contained. I didn't think anything of it, being that she's alway out for abou that long. I come back to find that she had dropped pellets all over the floor. She then repeated the action today and yesterday. The most she ever dropped was maybe one or two, previously and every time she did I would reduce the size of her pen, in case too much space was the cause. I have a tarp that runs the length of the cage, tucked under and around to keep the mess to a minimum. After this last time, I got frustrated and lifted her kennel to pull out the tarp so she'd have a safe space to scat. Well, mindlessly, I forgot she was in there when I did. It was only after I realized that I had been cruel. I couldn't hear her so I kinda entered the cage to make sure she was alright. Then she jumped onto her shelf and began thumping. Just about every thirty seconds. So I immediately pulled a sheet over her cage, turned off the lights and left the room. It's been an hour and now I'm back in the room and I just heard her thump. I sleep right next to her and the cage is too big to move. What can I do to calm her down? I know how dangerous thumping on this scale is. As for the rest of the litter box stuff. I cleaned both it and the whole cage and again she pooped all over. Did I mention that she already has hay in her box? What should I do tomorrow. Will she stay scared(she'd 8mos and super sassy adventurer most the time, not timid usually) of me well into tomorrow? If that's the case how do I let her out for exercise or to clean her litter. I heard shifts like this can indicate illness, is it worth going to the vet. I'm in school and pretty broke so something like that takes a lot out of my pocket.
 
Rabbits tend to drop poos all over the floor as a way to kind of leave their scent and mark their territory. They aren't too bad to clean up as long as they aren't the "wet" variety (which they should be eating, but our female sometimes steps in them and drags them all over the place). As far as thumping - it means they want something or there is something they consider dangerous. Our rabbit will thump if we forget her pellets, or if something can be seen from her cage that she is afraid of (like the vacuum or something that one of the kids might have set down), or if she is upset. Obviously she was upset about her kennel being moved with her in it, and if other things were shifted around, she might be upset about that as well. Check to see if there is anything that she seems focused on, or seems to be scary to her. Are you spending time with her and trying to kind of bond to her? It might also be that you entered her cage area, and if that is out of her normal range of what happens, that might have upset her. She won't stay upset, but I wouldn't worry about the two things you mentioned. One of our buns used to drop poos everywhere. What we did was we had a broom and dustpan and we would sweep them up and put them in his box so that he would understand that is where they went. We found out because of his size (he was a Flemish Giant), the poos were sticking to his fur and they would fall off when he was hopping around his cage, so he wasn't pooing everywhere on purpose. Now, if they start peeing out of their litter box, that could be a sign to me that something is wrong. One thing to keep in mind, females who haven't been fixed can have hormone surges at some point which can cause a difference in behavior.
 

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