I'm not sure where it would take the old .ini data from if you are using the correct ID file and have also modified the notes.ini. The ID should rule all in this case. Perhaps there is a registry key you can change, but I am not aware of one.
For this case, the problem might have been generated in the serverkeyfilename field. I think the names.nsf contains a configuration document which specified the serverkeyfilename in the notes.ini variable
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