Missing many tracks, not sure if it is iTunes/IOS5 upgrade issue or not.

I have updated iTunes/IOS5, and now lost many tracks. I play my music through a Lacie EHD via AEBS, but now appear to have lost many tracks. Apple store consolidated my library as I was able to play music previously, all of my music even though I couldn't find it when you went to search for it on the external hard drive. The Apple store weren't sure what had happened, but consollidated the library and it appeared to have found the music again, however, since I have got home and tried playing, the exclamation mark comes up on absolutely tonnes of music tracks, and I now cannot find them. I had been using Time Machine until about a month ago, but this I am guessing wont help because the music was already on an EHD. Does anyone have any ideas on where the music could have gone to or how I retrieve them back as I have some of it backed up to disc, but the last time this was done was about 2 years ago. Surely there is only so much back up of a back up you can do??? Please help?

This is a very strange problem. Latency is when say you pluck a string on a guitar and hear it through the monitor a little later.
The only thing I can think of in this case is if you changed the tempo and it messed something up.

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