Hi there.
We had once success with the following workaround: simply subdivide again to the level in question. We had the level there. The critical information about layer is missing in the docs (afaik) that you have to exit the layer before you want to do any layer operation. If you created a layer, you’d working on that layer even if you switched levels, unless you quit the layer on the level you created it.
The other solution is to export each level you have, and rebuild the ZTool level by level, importing the exported levels. That’s cumbersome but 100% efficient.