Hi Kees, APP uses filemapping for stacking (which on a SSD is really fast), you need to work on a partition with enough space. For 100 bias of your Canon 6D I suspect you need only 10GB of free space, which shouldn’t be a problem I think?
Also try to work on your fastest drive, this will speed things up.
I’ll check if I can prevent the crashing of APP if there is no more free space.