software-properties-gtk launches a dbus service 
/usr/lib/software-properties/software-properties-dbus
This service loads the sources in memory and edits them from there and saves 
them on a change.
The service keeps running after closing the software properties.
If you change things in /etc/apt/source.list or /etc/apt/source.list.d, these 
get overwritten by the values when first launched software-properties-gtk + the 
changes you make there.
If you f.i. remove a source from source.list.d, software-properties-gtk 
indicates this correctly as deleted. But if you edit something, the file 
magically reappears from the dbus service.

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https://bugs.launchpad.net/bugs/879943

Title:
  Synaptic messes sources.list and sources.list.d

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