One side of our 24x12 colony went the entire first year before being cleaned out. That side had a compacted limestone floor so moisture could travel out. We put down pine pellets, shavings, and 4 bales of straw and then didn't touch it. The top 3-4" seemed quite clean, the next few inches were a bit full of rabbit droppings, and it wasn't until the last layer against the floor (anything that can absorb moisture is also going to bring up moisture keeping everything damp) that we found mold. Prefer not to do it that way again though. It turns in to more work since it took a good month to get down through all the accumulated bedding and waste to the floor and we had to be careful not to leave areas of mold uncovered.
I like the side of the colony with heavy rubber stall mats. I put down pine pellets where they are most needed and then cover in several inches of shavings. The area around the hay silo is stripped every couple weeks to remove peed on hay and that is where lots of pine pellets are placed in order to avoid them ingesting any moldy hay. The rest is stripped every 2-3 months. We are trying similar on the other side now with part done in excess stall mats and part temporarily covered in plywood for now but we used more pine pellets than the other side so we could put straw on top. Straw and hay insulate moisture leading to things remaining wetter if you don't keep something absorbent underneath or keep removing it. That side is where most of the nesting is done so they appreciate the straw while the other side is most of the food, water, a cage stack, and a pen with the occasional nest from a lower ranked doe who could not claim the more ideal territory. I'm planning to clean it out more like 3 times a year instead of once and hopefully not accumulate everything as badly.
Colony rabbits do not seem to litterbox train well. They may pick a corner to make more of a mess out of but odds are they'll pick many corners and edges making it hard to spot clean unless you are talking a small colony with only a doe or 2.