Hi,

  save markings only saves what was changed

  if you want to save a full list you need to select save markings as
and check the checkbox around "save full state, not only changes"

  does this not work ?

** Changed in: synaptic (Ubuntu)
     Assignee: (unassigned) => Koen Beek (koen-beek)
       Status: New => Incomplete

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synaptic won't save selections
https://bugs.launchpad.net/bugs/156284
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