Try the grates but they have to sit right in the soft litter material so your rabbits will still feel like they are on an absorbable surface. NIC grids work well for this if they fit your boxes well.

Hi Katie {{{strength vibes}}} for you – I know how frustrating this can be.
With the carpet, have you treated the spots with a urine cleaner? Something like Natures Miracle or a enzyme based washing powder. I don’t know if more carpet on top will mask the smell as they have much more keen sense of smell than us.

How are your cages set up in relation to the others? That 6 of 7 are losing habits seems points to some sort of territory behaviour. Could it even be related to the season. (even fixed rabbits can have fluctuations in their hormones at certain times)  I wonder if hormones can effect a group of rabbits? Like hormones in humans can effect others i.e. women whose cycles synchronise. 
Have you changed anything in your cleaning routine? Any visitors or new pets in the home?

As far as the digging goes, there are grates that can work well. We also sell grates for litter boxes in our store. There are also litter boxes that are either covered or the kind that have an extra lip that folds in (normally it’s detachable) so that even if a bunny digs, it doesn’t come flying out.

I know with bunnies that are not all bonded, there will be some territorial marking that may never fully stop, but they can go through poo battles that can make things extra messy. I suspect the longer days of summer can get even neutered/spayed bunny instincts into over drive so that may play a part in some bunnies.

I recently had more problems with Jack & Vivian urinating outside of the box (many reasons for this that we are working on and they are getting better) but during this time, I went to home depot got plastic floor runners and covered the areas that were getting urinated on. If you find that the whole carpet where their pens are get urinated on, you may need to get some sheet vinyl or something for their flooring to save your carpet and make it easier to clean.

Good luck!

What are these grates for litter boxes? my buns go very well in thier litter boxes but they also dig in them!

It sounds territorial to me too (even though I am a rookie compared to others here). My bunnies live seperate but when I let my male out, he immediately goes over to my female and marks by her pen. I stop him now that I’ve caught on. I thought that this would stop once I got them spayed/neutered but I was told that he may still do it at times. The hormone comment makes sense to me. Have you thought about buying lenolium instead of carpet? I’ve been told it works great. You can buy the peel and stick lenlium squares pretty cheap. Then, it won’t absorb so it won’t smell and you can easily clean it up.