Hey Frank,
This is a bit of an obscure issue, but I've noticed that Autoptimize removes backslashes from HTML comments, even if HTML minification is completely disabled.
We put a bit of ascii art in the header of all websites we build. I noticed that the ascii art was broken, which led me to find out Autoptimize is the cause.
Also, the "Keep HTML comments?" setting still messes with the comments a bit - some newlines are getting removed. Other's aren't. I can't figure out why.
Any ideas on how I can resolve this?