Just to restate some earlier comments in the thread - kiwidude will correct me if I'm wrong as he's looked at this more than I have:
When the well-formed check was Off in the older versions, Sigil was actually automatically cleaning your code when it switched to Book View or Saved. So you could have potentially lost data. It was also checking if your code was well-formed too often. Sigil always cleaned your code when loading - again causing possible data loss for invalid EPUBs.
Sigil will now only check if your code is well-formed if it has to (switching to BV, saving, running certain actions). If it is not well-formed you must fix it before doing one of those actions. Saves the confusion of when to use it and wondering what its doing when off.
Saving code that is not well-formed could result in data loss when Sigil loads the EPUB again - because it cleans the code as it loads regardless of your Clean Source setting. So that's why the options are as they are, and won't change. With all the push to stop crashes and data loss, it seems obvious we also need to prevent corrupting data on save/load.
However, the question of whether or not its possible to save the code as is and pick up exactly where you left off without Sigil parsing the files is a question for later. It is not something that will be in 0.6.0. It may (or may not) be technically feasible (well, its certainly possible but its a question of how much effort it takes and how much it impacts things), but it would take time to work the details and find a way to avoid confusing users.
Last edited by meme; 10-06-2012 at 03:37 AM.