I (and others too) have the same problem. It is not one of files disappearing because in my testing I found that one can format both the card and the main memory, load some books using Calibre and "Removing" lines may appear in Collections on the T1 even though all the books loaded also appear correctly in the collection i.e. no books have been lost. The "Removing" lines in Collections are each counted as a book so giving an inflated total of actual books in the collection.
It is also not limited to the card as I get it, but less frequently, with collections of books in main memory as well. Differentiation between the card and main memory on my T1 and with Calibre libraries is along the lines that in Calibre I have 2 libraries one of which I sync with the main memory and the other with the card.
I had some suspicion initially that it may be related to the T1 PlugIn's mishandling of multiple tags and series against a book but I am now pretty sure that is not the case.
My suspicions currently lie mainly with the T1 getting confused in some manner with its handling of the book.db database in each of the main memory and card or (but less likely) with Calibre's loading and unloading of books - at least when "loading" because I found that the problem can appear when all one has done is load books onto a bookless reader. EDIT: If this is so then the problem likely only exists when the T1 has a card.
However those suspicions are numpty based as I have no knowledge of the workings of the plugin or the T1's management of the books.db databases. Which means that I have come to a dead end in trying to resolve the issue.
Last edited by AnotherCat; 05-20-2012 at 02:27 AM.