The published engine checks to make sure that script files haven't changed (to stop hacking and virus problems). So you can't release script patches and still use the original engine.

The good news is that the engine itself is fairly small compared to most people's content (about 1.5MB). If you are going to release a patch, you can just include the new engine as well. You will probably want to do this anyway since we (Conitec) release updated engines every couple of months.