jonny, Yes, this is one of those bugs that has happened to me too many times in the past, this includes the 5/6 buttons I keep on top of my timeline. A backup can be made and saved of the buttons so that if they disappear you can just reload them. A way to save favorites so you don't have to go scrolling through a million plug ins is to create a new project and name it Favorites. Put a few clips on the timeline and add all your favorite filters and transitions to these few clips.
Then, should they disappear again, you can open this favorites project and simply go to the clip's filters tab and drag them back up to your favorites folder. Do the same with the transitions you put in the timeline as well. Much quicker and you don't have to trash preferences.
Since I have to test and review so many softwares and third party plug ins I make it a habit to always repair permissions both before and after any updates or downloads. I repair permissions as much as a habit as I do command/save
Steve