You need to save your flag list.  Go to Collection --> Flags --> Save Set.  When you start the program up again, go to Collection --> Flags --> Load Set.  Just save again before you close the program if you make any changes.  This also allows you to different flag lists.

Alternatively Tags are like permanent Flags.

Set up a Tag called 'Cases':

Set Tags windown -> Left Click -> Edit Tags -> Add Tag -> 'Cases' -> OK -> OK

Then Flag all the titles in cases and do:

Collection -> Flagged -> Edit Tags -> click on square by 'Cases' -> OK

The you can clear the flags and the Tags remain permanently.

You can use the Tags filter to show only the Cased or Foldered titles (one click shows all with that Tag, a second click shows all without that Tag, a third brings it back to 'ignore')