In many cases, authors of Original works remove them because they are publishing them, although in this case I can't say for sure, but I have no record of it having been removed by staff for any reason.
I think you're fine moving it to Harry Potter - Slash M/M - Harry/Draco. Anytime you're going past the time frame of the books, you're pretty much in AU/AR territory anyway, and it becomes a given.
I'd highly recommend the copy/paste from Word or Open Office/Libre Office myself. I've been using that method with great success, and without any wall-o-text issues. I've never had an issue with formatting (other than centering for some odd reason) being lost, and editing after publishing is equally simple.