First off, Scrivener is a Mac software program, so won't help with even the most organized story effort if that effort isn't being written on a Mac :P. Secondly, Scrivener, or any decent writing program, excels at helping you organize layers and layers of work. My old AST binder in Scrivener's a mess, but it still worked because Scrivener let me put stuff down wherever I wanted or needed it, and arrange bits and pieces in whatever order suited me. For the software you end up using, the idea is that it should help you concentrate on writing as well as help you keep up with notes and stuff.

And do NOT delete anything, even if you don't use a writing program to help you plan stuff out. Just go through the whole set of folders and transfer anything that feels relevant to the new folder you're working in, and organize or write from there.

Also, my epic is Deathly Hallows compliant
Haha, you're now in the same leaky boat as I am :D. It has been surprisingly fun to work with new canon, thankfully. And it's been more useful to the story than I thought. One bit that I thought I would never want in (the Severus/Lily backstory) fits in quite nicely, and has even helped shore up some actions on Severus' part.

As for stuff that I don't want in the finished fic/series, I don't want pretty much exactly the things you don't want, and I'm trying to put the Horcruxes and Hallows firmly to one side as potential plotlines-- I think the social reasons for the Second War are way more interesting to work with, especially for groups not really mentioned or paid attention to, despite their significance.

I left HP fandom in favor of Star Wars
Ha, didn't know you left for Star Wars in particular-- I mostly just figured RL was eating you, or something ;). And I am actually glad that you didn't start up again with AST-- most of it is all right, but the backstory issues meant I was eventually going to run aground someplace, so the version that's up will never be finished, and the storyline I was heading for towards the end is probably not going to show up again. The only reason I didn't run aground earlier was because I was still following the canon event timeline in the first half of AST's sequel, and that freed me from needing to think back and work stuff out for my own universe quite as much.