You haven't read the article yet, which explains this. The key point is if they have been "deactivated" by the "Bashed Patch" build process. If so, then you just need to enable "ghosting" of them. That automatically adds a ".ghost" extension which prevents the game from seeing them and they don't show up in the "load order" but are still available for the BP process. If they are not related to the BP, then they need to be moved to get them out of the way. So, the basic BP process (once you have enabled "ghosting" in Wrye) is:
1. Adjust & Sort your "load order".
2. Mark Mergeables.
3. Build the BP.
4. When prompted, select "deactivate merged". (This takes care of everything else: all the needed "active" files (including the BP) are already selected.)
5. Run the game.
The next time you adjust your "load order": repeat steps 1-5 again.
Edit: Re transparency. See "Issue - ENB Transparency or Translucency problem" in the previously mentioned "Conflict" guide section.
Edited by dubiousintent, 27 May 2020 - 06:42 AM.