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Pomtroll, it's ok to be confused. We are throwing a lot of different ideas at you. It has got to be more than a little overwhelming, especially when the Sony is new to you. We've all been in your position before. Good to know you are on a Mac, that's what I have too.
If you delete the media.xml file, then it will erase all your collections currently on your 350 and start fresh. The negative is that I think that you will lose any of your notes and bookmarks, etc. I would make a copy of the media.xml file before you delete it. For example, place a copy on your desktop. You shouldn't need the backup copy, but it's usually a good idea.
I don't think you should do anything with the metadata file. I just wanted to know if you had one. Since you have a metadata.calibre file that implies that at some point you had your ereader connected when calibre was open. I still think that calibre is the likely source of all your collections. Here's a test you can try. I would open calibre (when your ereader is not connected via USB). Here's what I would look for in calibre. To begin with, make sure that you have selected the icons in the lower right corner of the calibre window so that you "Show Tag Browser" and "Show Book Details".
1) In the box in the left of the screen (that's the Tag Browser), do you see an item called "Tags"? For example, I have 45 tags. If you expand the drop-down box under Tags, do any of the names look like the names of the collections on your 350?
2) Are any of the books in your calibre library list the same as the books that are on your 350? If so, click on the book to highlight it. In the window on the right of the screen (that's the Book Details) are the tags listed that look like the collections on your 350?
If the answer to these 2 questions is yes, then calibre was probably the problem. You could edit the metadata for your books in calibre to delete all those tags or simplify them. Then the next time you connect your 350 with calibre, it won't try to recreate any of those random collections again.
I think that you are probably not syncing with Reader Library if you aren't sure. I have a sync folder on my 350. In the Sync folder that you found, I also have a file called sync.xml. When I right click on sync.xml and open with TextEdit, then I see a list of all of the collections which are being synced between my 350 & Reader Library. If you don't have a sync.xml file in this folder, then you aren't syncing collections.
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