iSilo maintains a database in the handheld's memory that stores the document list information. Whenever iSilo starts, it searches standard locations on mounted memory cards for new documents and adds entries for them to the document list. Each entry stores the document's name, location, and settings. The document's name and location uniquely identify the document. The settings include, among many other things, such things as local bookmarks, display settings, and the document's category.
For the purposes of this explanation, an external document shall mean a document located on an external memory card.
iSilo never automatically deletes entries of external documents even if it can not find the document on any mounted memory cards. If it did delete such an entry, the document's settings stored in the entry would be lost. Only if you delete a document explicitly from within iSilo does iSilo remove the entry.
Remember that the document's name and location uniquely identify the document. The location consists of two parts, the name of the card on which the document was found and the path to the document on that card. The name of the card is known as its volume name. However, it is a likely scenario that you may have two cards with the same volume name. This occurs if you have not given each of the cards unique names. Assigning volume names to cards is outside the scope of this document.
In order to properly support the use of multiple cards regardless of whether or not two or more cards have the same volume name, iSilo does not automatically delete entries of documents it can not find. Given the manner in which iSilo maintains document settings, doing otherwise would mean that you would lose information.
What all this means to you is that if at all possible, you should use iSilo to delete and rename documents in the standard locations rather than use a third party file management utility if you want the document list automatically updated to reflect the changes.
The current solution is not ideal and warrants improvement, but it does prevent the inadvertent loss of information when using multiple memory cards.