Two libraries on one drive, music co-mingled, want to separate:

Here is my situation:
I have two libraries, lets call one Lossy, and the other Lossless.
The Lossy library is ~140GB of 192-364kbps AAC files and a few mp3's. I use this library to sync all the family iPods and it also has all our ripped and downloaded movies and TV shows that feed the Apple TV.
The other library is all my CD's ripped to Lossless ALAC files. Music only.
I initially was forced to move the first (Lossy) library to another drive as the main drive was full. I have four drives on my computer, so no biggie. I used the methodology outlined in the tutorials and everything went fine.
The iTunes library file for the lossy library remains in the main drive in the iTunes folder. Only the media file is on the secondary drive.
When I started ripping my CD's to lossless format, I placed the iTunes library file on the same drive as the iTunes Media folder for the lossy music, but designated a new folder (Lossless Music) as the media folder.
iTunes outsmarted me, and without my noticing, it put the music media into the existing Media folder on that drive. To compound matters, I didn't double check the Library name when switching back and forth, and iTunes started calling both libraries Lossless. The result was that Lossless files started to infiltrate my Lossy library.
So basically, for the most part, when I select the Lossless library, I get mainly Lossless tunes. However, when I select the Lossy library, I see a lot of Lossless files.
So, I figure I need to physically separate each library to separate drives. I moved the Lossless media to my HP Windows Home Server, however copies of most of the files remain on the previous drive (ie they were copied to the WHS).
I would like to completely separate the libraries and get all the orphan files that sit on the main drive (used by iTunes when the resident drive that the Media Folder resides on doesn't respond fast enough). If I use a vacant drive and move the Lossy library (and accompanying music, movies, TV shows, Apps, et al) to the open drive, do I run the risk of polluting that library with Lossless files that share the old media files folder? ie does hitting "Consolidate" include every file in that folder, lossy and lossless?
If there is a risk, any suggestions for a methodology for separating the lossless from lossy files and then consolidating clean libraries?
Thanks, and I hope this isn't too confusing.
In the future, the Lossless library will only be on the WHS for playing by two Roku music players and a Squeezebox Touch.
Thanks and sorry to be long winded...

I prefer method 2
Using Multiple iPods With One Computer
but if you like method 1, read this too
How To Share Music Between Different Accounts On A Single Computer

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