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The problem is in the ambiguity between instances from cells from a cell tree (the instances inside the child cells) and the instance-expanded tree (also "instances of"). With "delete instances of TOP...*" the child cells are visited multiple times as "instances of ..." denotes the instance-expanded tree and at the second visit the error is thrown.
This refers to https://www.klayout.de/forum/discussion/2478
A test case is available.
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