There were a couple of bugs in the Paper UI regarding saving the system:links information, see e.g. this PR. Those fixes are available in distro 504, so I would hope that this issue is solved now.
I’m thinking is should have split this into 2 threads now
I agree, as I cannot say much about the second part 
I can only link to this discussion, which is also about documenting how to use things files with the Z-Wave binding - maybe this helps.