Managing two libraries in iTunes - weird bug

Question

I have two iTunes libraries (that is both library database and music files) that I am trying to maintain. On my internal drive in my MacBook Pro in which I have a set of AAC files with their associated library databse. On an external drive I am creating a "this is the last time I ever rip these CDs" Apple Lossless library (which can also serve as a backup).
To switch between these libraries I open iTunes while holding down the option key and choose the external drive library file. I then go into advanced preferences and redirect it to the music folder on the external drive. I then import CDs in lossless format as I have the opportunity. When I am done I switch back to the AAC internal library for everyday use. I can use this method to change between the libraries reasonably reliably. However, a strange bug keeps rearing its head.
When I switch to the external library it will commonly have references to AAC files on my internal drive seemingly replacing references to lossless files on my external. I can fix this problem by sorting by type and deleting all the AAC files from my library (this just deletes the references) then choosing add to library to reacquire the lossless files. This, however, is a pain.
Any suggestions as to what is going on and what the safest way to switch between these two libraries is?

Answer 1

Thanks for the response but still not working correctly.
I was not responding to you in my first post and I did not see I was responding to a someone other than the original poster. I'll go with it since it is relevant. If you ahve any further questions, please start a new topic in the correct forum.
The lossless version was at G:/lossless.
So you are on Windows? This is Forum*: Using iTunes for Mac* .
I started a new library the way you suggested
That's the only way there is to do it.
Create a new library and select completely different locations.
Don't choose the same location as the other library.
Do this.
Create 2 folders on the external.
G:\Music\Lossless
G:\Music\AAC
Hold Shift (for Windows), Option (for Mac) and launch iTunes
Select *Create new library* and select the AAC folder you created above.
This will create a new iTunes folder in G:\Music\AAC. You should now have G:\Music\AAC\iTunes\.
Go to Windows Exploder and move all your AAC files into G:\Music\AAC\iTunes\iTunes music\ folder.
Go to iTunes menu File -> Add folder to library and select G:\Music\AAC\iTunes\iTunes music\.
Quit iTunes and restart holding Shift (for Windows), Option (for Mac).
Select *Create new library* and select the Lossless folder you created above.
This will create a new iTunes folder in G:\Music\Lossless. You should now have G:\Music\Lossless\iTunes\.
Go to Windows Exploder and move all your Lossless files into G:\Music\Lossless\iTunes\iTunes music\ folder.
Go to iTunes menu File -> Add folder to library and select G:\Music\Lossless\iTunes\iTunes music\.
Next time you launch iTunes hold Shift* (for Windows), Option (for Mac) select Choose library and select teh iTunes library.itl file in teh folder you want.
Make sure you first set your Import prefs to AAC or Lossless, depending on which folder you are in.