Personally, I don’t see the harm – I haven’t played your entry yet, but it sounds like more of a bug fix than a new feature (the former of which is allowed, the latter isn’t).

Sounds like a bit of a new feature to me. If in doubt, probably the best way to go is to add the feature and provide a separate download to the new version, with it clearly labelled as being post LD. That way the people rating your game can decide which version they want to rate.

I personnally agree with Lucas Tridath. But don’t worry about keeping your LD submission as is : even if people are asked to vote the LD version, a post LD one will often be prefered to test the game and it will make judging more favorable.