Ok, I encountered this error again.
When I specifically right-click-hold on a checkpoint to remove it, it works just fine.
The error crops up, when I am already right-click-holding, removing nearby trees and rocks, and then pass over the checkpoint.
When I'm doing this, right-click-hold ignores mining ores, if I had removed a tree/rock before I pass over the ore patch, but it doesn't ignore your checkpoint, and crashes... so perhaps there is a state that isn't being accounted for there.
-- Smoov
