Two alternative options...
1) Zombies that dig, but do not leave holes. This would solve a lot of problems. Sure it'd look a bit cheesy as they dropped from your underground base's ceiling, but try to envision what a cheerleader zombie would actually look like excavating a 40 meter shaft into your base before plopping out of the hole. Seriously....even with crazy special effects, I just can't picture it...immersion destroyed.
For reference, the reality is that if you gave a cheerleader zombie hydraulic-like strength, she'd rip and tear into the dirt/gravel/ and err...stone (let's pretend), and sink into the loosened material. She'd have a female dog of a time "digging" and sinking once covered, but let's say she persevered. She'd continue downward, but there'd only be the circle of loose dirt where she began on the surface...no hole.*
2) Any holes dug by zombies during the Bloodmoon are "reset" after noon (the loose dirt, etc. has all collapsed back in on itself). This allows for the full horror of seeing your defenses being breached as well as surveying the damage in the morning, but conservation of mass is observed in the end. This would be like what we see with destroyed POIs in A17 regenerated by a quest.
*For legal purposes, I will affirm that I've never thrown a cheerleader into a dirt/gravel/stone shaft with digging implements to test any of this.
-Morloc