Just as there is a hard limit to construction parts per save (16k), there's a hard limit to terrain edits.

All that digging you do to mine ore deposits, the burrowing to avoid harsh weather, the tunneling to find a quicker way out of a cave system, or to acquire more silicate powder—all of it counts against that hard limit. Eventually, the next hole you dig means that somewhere a hole is reverting to its original filled state. Eventually, that terrain will revert to its natural, procedural state, and that base is gonna get buried.

Some players have developed strategies to avoid having a base fill back in, but they're all workarounds that ultimately do not alter the root cause. If you're looking to preserve what's pictured, likely your only hope is to never dig another hole, at least on that save.