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In general I do not think there is in Nazca a straightforward way of removing an object in Nazca.
A not so straightforward way would be to use the cell iterators (see this tutorial https://nazca-design.org/inverted-mmi-creation/) to rebuild the full structure filtering out the objects you do not need, but that would require some work.
If I guess right and you just want to delete the cell that was left empty by the removal of some layer at the previous step, I would suggest to create the cell with the
option. If a non instantiated cell is put in another cell, the content of the child cell will be put directly in the parent cell when you export, and so the parent cell will not be visible in the final gds.
I this in not what you have in mind, please be more specific about your problem and I can see if I can help.