I don't know entirely, I never investigated it to that extent. What I do know is:

1) Any scenario created with just the default files will work in any new setup you have. In other words, you can use it in any new mod you install. Once you do that though, you can never go back.

2) Most items used during the save scenario process will be required to use that scenario again. Items include things like sound & units and their definitions. Most missing items will crash the game as soon as it is loaded. Some will wait to crash the game until that particular item is needed.

3) I don't know about all code but I do know SLIC info is saved. When I first started changing SLIC, I found you had to start a new game from scratch to see any changes you made in the SLIC code. Making changes and loading a saved game didn't work.

So, in general, I would say most of the file info is saved and will be required. Disclaimer: Keep in mind, these are pretty broad statements, your mileage may vary. I have no doubt certain aspects can be changed without any problem but I found it much easier to just start a new game. It wasn't worth the trouble to find out what did and what didn't matter.

I have not investigated it fully either, but I have figured most of that. I have also added leader tga files and changed the name to a saved game...worked fine--didn't crash during diplomacy, meaning. I was less than successful with the changing of the civ name. Other than that, however, I have not tried much...