I have created the issue as a bug in issue queue of node clone module.
Any pointers on this?
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Your issue seems to be confirmed by some other users also now.
Comment #9 of that issue contains a patch that might possibly solve it.
Another possible solution (patch) is included in comment #8 of that issue, proposed by the module maintainer. With a comment like "Not sure about the use case ..."
The issue is currently in status "Needs review", so maybe you might (still) have an appropriate use case to get that issue in RTBC status?