Thanks for all the advice. Scarlet Rose you have an interesting point there. Since getting Dylan and finally bonding the two rabbits my rule about not reaching into their cage has relaxed a lot. This is mainly because they are both very timit rabbits, particularly Pepper, and catching them outside of their cage to groom them etc is pretty much impossible, so I’ve been taking them from the cage to groom them before letting them run free in the house – Dylan is heavily moulting. They have also been getting lots of trips to the garden with the lovely weather lately and to get them there I need to catch them, put them in the carry case and walk them right round the house to get to the back garden (the safest place way from neighbourhood dogs). So there is a lot of handling that they might not appreciate – all for a good reason I think. Now that the weather is getting better I am able to leave doors open to the rest of the house and I think pepper senses this as she has already started to follow me to try to get to other rooms – whereas in winter she knows not to bother. I’m not sure how I would go about retraining – especially as they are now both in the same cage.
Their litter tray is currently a cat tray which they can get in and out of easily and the high sides stop the mess coming out with them. They don’t pee outside of the tray, it’s just pellets and I’m pretty sure it’s just Pepper.
As for Dylans playful tossing this is not a problem and he has a lot of toys which tend to bounce on Peppers nose when Dylan plays with them.