Thanks for the reminder to use the "Give Feedback" feature. But what if other users have the same problem or suggestion or feedback? They aren't able to see feedback that has already been given this way and are unaware of what has been tried, or if there are any workarounds, or even if the idea has been considered and will later be implemented or discarded.
Yes, you're right about probably being able to just overwrite the settings with the actual text in the case of the mismatched character encoding. But I couldn't be sure that that was the only source of the conflicts. What if there were other "hidden" \uFEFFs, but in the text instead of the settings? I ended up checking out the unicode representation of each settings string in a different program and making sure the correct characters were used.
I can't answer the question about the source of the zero-width, non-breaking space. I doubt they are using AutoCorrect, but I can find out. My initial assumption was that it was introduced somehow by copy/pasting text, but I still don't know where they would have copied the text from other than Paratext itself. Maybe a Word document a long time ago (>10-15 years), if initial drafting was done that way?