Animate reads directly from the .html file, not the .an file. The .an is really just for preferences; you can even delete this file and open the HTML file in Animate and any external changes you make will be preserved.
What you can do if you don't want your changes to be reflected is create a new HTML file in your composition directory, copy over your Animate tags and make any markup changes there while continuing to edit the Animate HTML file in isolation. So you'd have two HTML files, one for editing and one reflecting any custom markup.
I can see that it's reading it, I just don't understand why it pays any attention to non "edge" stuff when opening your project. i.e. other than the "Edge Runtime" header script tag entries and the "Stage" div in the body, the rest of everything else has nothing to do with your project, so why isn't it just ignored by edge when opening the project?
So to find a work around...
my work flow.... I have a multi mon setup and usually work with Dreamweaver running at the same time. I usually edge "publish" directly to a Dreamweaver local "website" folder (I do this for several reasons but one is so it's very easy to update my online/offline "sandbox" servers from DW). I do this a lot when the animations are "single" html pages linked to from another page. So if I understand you right if I want to modify my html file I would have to publish to another location, when manually copy everything except the html from that location to my Dreamweaver location for previewing etc if I want to see the real final output (i.e. including the changes I made to the html for mark-up etc) ?
From what I can tell, when creating an edge project it creates the html file and as long as you don't change the actual file name, "Title", or "Class" id then nothing else ever changes in that file. So.....
Is there a way to "publish" to a folder and include everything EXCEPT the html file ?
I guess I could use a dummy name for the EDGE project html as long as my real html file used references to the "dummy" in the "runtime" and "Stage" Div sections? then I could continue to publish directly to DW ?? It's would be another set of names etc to keep track of.
It would be a whole lot easier if edge just ignored stuff in the html file that did pertain to it.
Thanks for your help