And there are non-zero chances that changing to the wrong option and saving the document will permanently break the file as the combination of two wrongly configured codesets.

I don't know, maybe it's me who's doing something wrong and turn to using only a small subset of software tools, properly configured?

But I do need to process documents from many origins using a variety of different tools; I've never found a good programable multimedia editor that satisfies all my needs (something like emacs but with WYSIWIG capabilities).