I'm sure I read somewhere that if you play back a replay of a battle and have different desynchronise settings to when the battle was recorded, the whole thing gets out of synch. So if that's true, don't go turning it on/off during a custom battle you might want to save.

Although I often have it on, I don't think it makes a great difference to the game experience. I always switch it off during large battles to improve frame rates as much as possible.