I believe the offending code is this: https://github.com/Chisel-Team/Chisel/blob/1.9/dev/src/main/java/team/chisel/common/inventory/ContainerChisel.java#L123-L128

I'm not sure what the point of that onPickupFromSlot() is, but if it's to update the chisel inventory, then you should at least temporarily store whatever is in the cursor and restore it after.