I've never had a problem with Calibre doing anything I didn't want it to do with my books either in the Calibre library or on my reader.
Did you possibly have the Sony reader software running at the same time? I've read of a few instances where that can cause conflicts (I never use the Sony reader software unless I'm buying a book from the Sony store, and then the program is immediately and fully exited after the purchase and Calibre is never running at the same time).
Edit: I don't have the T-2, but I know for my 350s, the metadata automatically uploads from Calibre to my readers everytime I connect them (through a setting Preferences, Import/Export, Sending Books to Devices, Metadata management at the top set to Automatic Management). But even if yours is set to manual, I would think on send the metadata would then be resent to your ereader and corrected.
Unless you're saying that within your Calibre library, all collections and tags were removed there?
Last edited by Ripplinger; 10-08-2012 at 05:37 PM.