I have a similar problem. So I left all the albums/files on my HD, but put some of them outside the "music" folder I've defined in most of the software I own as the "library" location. That way, I still have convenient access to them if I want to compare etc, but I don't have to scroll through them, under day to day circumstances, and they don't come up in "random" playback.
I moved the 87 CD's out and the various earlier mono versions I own, as it's pretty clear to me that the 2009 versions are going to be my "default listening" set instead of these. I heard secondhand that Dr. Ebbetts was quoted as saying the remasters make his Beatles efforts superflous.