I think you must have TaskPaper 2? Unfortunately TaskPaper 2 won’t work on macOS 10.12. A technology that it relied on (garbage collection memory management) was removed from 10.12… Oddly TaskPaper 1 does still work, since it didn’t rely on that technology.
You’ll need to upgrade to TaskPaper 3 (50% off for existing customers) for 10.12 support.