The sail barge transition I know was due to a few frames being trimmed for the new wipe. Since taking frames from the GOUT resulted in a significant drop in quality, Harmy opted for the slowdown effect using HD frames only. Even without access to better sources for those missing frames (which might be in the works), Harmy experimented with a better method for handling missing frames with the Han-Greedo conversation in SW 2.x (I think it was a "flow" something function in AviSynth, like frame interpolation on TVs, but not as artificial looking when you keep the framerate the same). He eventually got better sources so didn't need to use the other method, but I think even under the worst-case scenario, there's still ways to make this transition more natural without new source material.