Hi I don't know if I have made this happen or TC has just updated itself automatically, but My TC has completely reset itself like its a fresh install. I accidentally double clicked on an old TC drawing from 2005 and now all my settings have gone to default . I hope they didn't get overwritten. I also have light-works plug in too and that was set back to REDsk. also when rendering i get a box pops up and says there's no light-works data.
Unless you were missing an update the last update I got for 2016 was Jan this year, (probably general released in Dec 2016).
Have you logged into computer as a different user, if so, TC will show defaults because the 'new user' won't have access to your settings, they would still be there when logged in as correct user,
If it happened due to a fault or user error, - did you previously save your custom settings, tools menu - customise - options tab, workspace - save in, if so you can use 'load from' to get some stuff back to normal, you could do this if for example one clicked the default button by accident.
It is possible to locate the current user settings and built-in folder but chances are they got over-written when you opened and closed TC. I can't comment regarding Lightworks as I don't have it,