I don't understand question #1.
The Chilkat XML parser ignores comments when parsing, and therefore they are not present in the in-memory DOM (Document Object Model) after loading. The would also not be present after writing. If comments need to be maintained or accessed, then a program should use another XML parser (as there are many available with various features, strengths, etc.)
Thanks for the response, sorry for the delay as this is a side project for now. I did get a little further and will post specific questions under a new post. The info about comments was very helpful.