How to delete duplicates from iTunes but not hard drive

I'm running iTunes 10 and have my music stored on both my NAS drive and backup drive.  Each track appears twice on iTunes: once as lossless for streaming and and once as compressed AAC files for synching to ipods and iphones.
For some reason, when my PC is turned on after being turned on, the linkstation cannon be 'seen' by iTunes, and therefore if I try to play a track, 'the original file cannot be found'.  If I use the 'add folder to library' option in the 'file' dropdown menu, the tracks are located again.
Unfortunately, I the last time I did this it resulted in 4 copies of each song on itunes; 2 lossless and 2 AAC.
I have 2 questions:
Firstly is there an easy way to delete the duplicates from my iTunes library so that I am left with only 1 lossless and one AAC copy, but not deleing the files from my NAS and backup drive?
Is there a way I can just store my music as lossless, but convert it easily to aa more compressed format for synching to iphone and ipod?
Thanks!

You can try my new DeDupe script. It should be able to get rid of the redundant copies while keeping one copy of each track in each format. See this thread for background.
I've not used the feature, but iTunes can downsample to 128k AAC on the fly as it syncs your devices. Of course you might find the process is too slow for your needs or find that 128k is too much compression.
tt2

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