If a file is modified in a library that has SharePoint content approval enabled (including those using SmartLibrary workflows), the file will drop back to a pending status and disappear from the "All Documents" view.
Unfortunately there is nothing specific SmartLibrary can do to prevent that situation because it is SharePoint behaviour. However, you could potentially use the "Secondary Publish" option to copy the approved files to another library in which the users only have “Reader” access (and can’t edit a published file) and without Content Approval enabled.