My preferences where the default, 'use_gio_unsafe_file_saving'. I tryed the 
others, and can conclude:

- 'use_gio_unsafe_file_saving' checked, with 'use_atomic_file_saving' 
unchecked, does not save to an existing file, but does save to a new file
- 'use_atomic_file_saving' checked, with 'use_gio_unsafe_file_saving' 
unchecked, does not save to an existing file, but does save to a new file
-  with both the above options unchecked, geany itself does save to both 
existing and new files

This is strange behaviour, because according to the link 
[(https://wiki.geany.org/config/all_you_never_wanted_to_know_about_file_saving)]
 'use_atomic_file_saving'  always writes to a temporary new file first, and 
then renames that to the name of the existing file. So at least the temporary 
file should be available after fail, but it is not.

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