Mielr: I started listening closely to that scene because you pointed it out. ;) There is definitely a music dropout in the left channel just before Luke cuts off Vader's hand, which is fairly jarring once heard. Then I went to the 35mm mix and found that this same dropout is also present there, but for some reason it is much less noticeable. At the same time, I found that the balance of the 35mm version was superior in that scene, because the lightsaber sounds in the 1993 mix are too loud. They don't drown out the music, but compared to the original mix they push it out of its prominence somewhat.
So not only will the 5.1 make the dropout less audible, but the scene's epic music will come through more clearly. It's a win-win.
dark_jedi: Do you mean the 35mm stereo mix of Empire? The early version you made that I listened to had a noticeable gap in the sound when the door slams shut behind Luke as he enters the carbon freeze chamber. I don't remember offhand if there was an LD side break there, but if so then missing frames would be the likely culprit. There was also some hissing during the silence before the start of the main title music, and the very beginning of the file had a bit of something else on the laserdisc before the movie started. I seem to remember you saying you'd fixed those things, but I haven't heard a corrected file.