I converted HappyLee's TAS of Super Mario Bros. from 2011 from .fm2 to .bk2, the inputs are exactly the same but instead in 17867 frames. (BizHawk appears to have one frame less of lag compared to FCEUX in Super Mario Bros.)
Yep, I have tried converting the SMB2J TAS and it desynced as well. I'm not exactly sure when it desyncs but it does.