DoN's 3D-Pathfinding / Flying-AI system (with full source!)

Ah! I missed this part. A huge voxel size like 2000 only makes sense if the minimum distance between any two obstacles (relevant for pathfinding) in your map is also of a comparable distance.

Just turn voxel visualization on, walk around your map. If a single voxel is so huge that it encompasses multiple obstacles then pathfinding will simply not work for those obstacles.

So try lowering voxel size and see if it resolves your immediate issues. You’ll also need to increase grid size along X, Y, Z accordingly to compensate AND increase query-timeout and/or max-iteration values to allow for enough room to calculate the path (smaller voxel sizes require a greater number of nodes to cover the same distance and therefore are more expensive in terms of performance)

If you’re worried about longer load times for your large map, consider using the infinite-worlds experimental feature I talked about in a previous post.