If you're encoding a TAS of Tetris that uses pausing, use Game Genie codes that keeps stuff shown while paused for a separate encode.
Game Genie codes:
CEC-30E-C45 Keep Stack Displayed While Paused
Address 1C30 Value CE Domain ROM
D9C-53E-D5D Keep Current & Next Pieces Displayed While Paused
Address 1C53 Value D9 Domain ROM
If using both codes and there's no desync, then it's perfect.
If both codes cause the movie to desync, encode with the former code, and encode with the latter.
If the latter code causes the movie to desync, then you're fine.
If the former code causes the movie to desync, then you're screwed.
If using either code separately (not both together) and there's no desync, then both encodes have to be put together for a 3D encode.
To encode in 3D:
Use the former code and hide the sprites for encode 1
Use the latter code and hide the background for encode 2
The 2 encodes have to be combined to make a 3D encode which can easily be done on YouTube.