ncs-netsim is using file netsim/.netsiminfo for all operations. Assume you have 8 devices c0,c1,...,c7, now you want to delete only device c5 (which has index [5] in .netsiminfo). First delete the block "##device c5" in .netsiminfo. Now total number of c/c* devices becomes 7: they should be numbered continuously from 0..6. To fix this, just move the last block of "##device 7" to the original position of "##device c5", and rename all index [7] to [5]. Now device c5 is successfully deleted. Optionally delete netsim/c/c5 folder.