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/ddf06e8a1ce945a9d3dbdf482dc9aeb8...

**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 } ```