Ah yes. This is a consequence of writing our nodes on top of Mayas Deformer API.
Are you using Ziva's menu to safely delete objects? The corresponding MEL if you're scripting:
If you are, right now I can't reproduce it in Ziva 1.3. For me there is always a set connected to the embedder that stops it from being deleted when the last tissue is removed.
Can you try it in a fresh scene:
Make a sphere, make it a tissue, run Ziva > Delete selection.
Make a new sphere and try to make it a tissue.
If that doesn't work it would be good to know which version of Ziva you're using and which version of Maya etc.