This same situation - empty project in project explorer, and the null pointer exception - was an unwelcome greeting coming home from a long holiday. We need to face it that projects livingin the MCUXpresso world, as with its KDS predecessor, are living on borrowed time in an incredibly fragile tightly coupled dev environemnt. We're always on the edge of something breaking that'll eat half a week. It's not you.
Points to NXP for at least providing a sort of cross platform IDE but all points come off because the breakage happens way too readily. I never have these problems in IAR or even with the bloated junit IDE for android development.
First you need to recover your workspace. Something toasted it. Hopefully you take frequent backups of the workspace. If so you won't need to re-create the Segger config, it'll still be there.