It wouldn't explain the loss of all category data, but have you tried playing with the size of the database? (I believe you can reach it through the "Settings" menu in the document view.) The default size of 100K won't be large enough for so many documents.
Also, why don't you specify the default category for the document when creating it? If you specify the Default Category (under Document Properties/Document in iSiloX), then the category becomes a part of the document and shouldn't be lost. While you are only limited to a single Default Category, it would be better than Uncategorized.
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