What I'm doing for my project, which isn't currently designed to go online but would be able to easily enough, is to package game data into Lua scripts. For example, a spaceship definition might be added to a list like so:

ships[rama] = {  mass = 10000000;  thrust = 20;  turn = 10;  graphics = 'images/ramapack';" And other bits of data about the ship}

At startup, the game simply loads all the Lua files it sees, and then calls a set of Lua functions which take these lists of game data and instantiate objects based on them. The neat thing about this is that you can load a Lua file whenever you like. If I wanted to add more game data to the game mid-play, I could simply put another file into my data/lua directory and then tell the game engine to load the file; it'd immediately become available for use.

In your case, you can just download the new file, add it to your Lua (or whatever) directory, and then load it. If the new file replaces an old one, then (I believe) loading it will simply overwrite the old logic so long as the load doesn't do any append-style actions.

Note that this mainly works because the vast majority of the game logic is also in Lua; the C++ engine that loads Lua files doesn't do a whole lot else (largely asset management, collision detection, and the like). If you needed to change something in the base engine, then you'd be forced to download, apply a patch, and restart.