There was a new version of iTunes recently (last couple of weeks) which seemed to involve not just a rebuild of the iTunes database (itunes.itl) but also a visit to each music file - or at least that's what I think it was doing. I suspect it was visiting each file to gather previously ungathered tag information to put in the database. When you download, that's the version you will get.
Go through the options and set them how you want - as mentioned above, iTunes can either copy data files into the default location or not, as specified. If you have lost your iTunes database, best bet would be to got to Edit/Preferences/Advanced, change the location of your iTunes media folder location to where you want it on your C drive, check the box Keep iTunes Media Folder Organised and Copy file to iTunes Media folder when adding to library then do File/Add Folder to Library, point it at your backup then let it copy all the files and build the database at the same time. (NB It does a copy, not cut)
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Restoring from a back-up drive - any tip.. new