In the SaveSettings function (lines 488 to 495) -- if the file details are stored in separate files it will also be written to settings.conf --

https://github.com/geany/geany-plugins/blob/ddf06e8a1ce945a9d3dbdf482dc9aeb8478f080c/geanynumberedbookmarks/src/geanynumberedbookmarks.c#L488-L495

Unless this is, by-design, I think that the following change to the while loop will make it so that the bookmarks are only stored in settings.conf if separate files are not being used

488    while( (fdTemp!=NULL) && (WhereToSaveFileDetails==0) )
489    {
           [...]
495    }

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