Well then it's very odd how this could happen, isn't it. 
Is this your save? Was it made on someone else's server?
I made the build, on my server.
This happens alot.
I'll save, start up later, and load it.
I'll save 65k bricks and end up with 44k bricks out of 44k bricks. so its not like it was 44,000/65,000
So it can't be stuff being disabled.
ITs like its not registering or saving them.
Maybe its because of the distance?