Tried asking this on the FLAC forums, but it might be more a f2k issue , so: how can I get Converter to delete an input flac file , after converting it to another flac file (e.g. to convert to a different version of flac or different compression setting)? I see no option for doing it using the preset FLAC encoder, nor have I been able to get --delete-input-file or -f (force overwrite) to work as parameters in a custom commandline FLAC encoder, using either stdin (-) or %s as input.

Converter cannot delete the original file, you have to manually delete the file(s) after conversion.
By the way, flac.exe will never know the original file's name (because flac.exe is feeded with a temporary one), hence it cannot delete the original file.