In the past, I was experiencing a random change of the theme in TaskPaper. Somewhere between a couple and a dozen times after opening TaskPaper, the theme would change from my custom selection (JK.less) to the default (Light.less).
This persisted even after I deleted Light.less.
Recently, I decided to consolidate my purchases to Mac App Store versions (I prefer the MAS method of updates). I bought TaskPaper from the MAS, and deleted the old version.
Now, my theme never changes! Hooray!
Just an FYI, in case this helps someone else who is frustrated by the random theme changes.