When Rucy was alive, she and jack were almost perfect, but every once in awhile, I would have to put them through a littertraining refresher course. Sometimes there were things I knew had set them off – the smell of other animals, visitors etc. Normally territorial poo markings are a reaction to something (especially if the bunny was litter trained before), so if you can identify any changes or anything that may have set her off, that will help. however, sometimes, I couldn’t figure out what made my bunnies lose their habits, so then I just did the “refresher course” which consisted of:
Limiting their freedom completely to an xpen for a week or so. This helped them distinguish THEIR territory from the rest of the house. I also made sure to put lots yummies in their box – like little itsy bits of shredded carrots, or a raisin cut up into 4 little bits. (That way there are MORE pieces without over-dosing on the treats.) You can also put some of their favorite greens in the box too – just anything to encourage them to get into the box.
Then when you do finally offer some freedom, just be persistent with supervision for a while.