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As soon as we started using a new canned theme, we noticed some odd behavior within the Magento admin area - after edits to a product (like inventory or price changes), that product was removed from all its categories.
After checking the code, we noticed that the function $this->getCategoryIds() (in /app/code/core/Mage/Adminhtml/Block/Catalog/Product/Edit/Tab/[url removed, login to view]) was returning an empty result instead of an array of the category ids the product was assigned to. When Magento saved the results after an edit, it used this data (an empty set instead of the correct data) and wiped out all the sku to category assignments for the product.
Need to locate the issue and resolve asap