We often advise users not to choose Process only updated subdirectories under the Advanced » General options (subdirectories = folders). In some cases, the reasons are obvious, but sometimes they aren't.

First, a number of the popular bundled skins, like Tiger and Photoblogger, control many album functions with JSON database files. If you process only the updated subdirectories, you can easily end up with JSON files that no longer reflect the actual contents of the album. This produces a broken album that fails in odd ways, and it can be difficult to understand the failures. In short, if using a JSON-driven skin, this option should almost never be chosen.

With any skin, if you've updated the skin, but made changes in only one or two folders (adding images, changing captions, etc.), you can end up with some pages that are made with the older version of the skin. But all the pages are sharing the same resource files, like the CSS and JS files, and this kind of version mixing can be disastrous.

Similarly, if you've changed some skin settings, but again have made changes in only one or two folders, you will end up with a mixture of pages within the album. Some of the pages will reflect the changed settings, but others won't, which is almost never the result you're after.

Finally, there's another situation in which this setting can produce puzzling errors. If your project contains objects that don't have thumbnail images - PDF's, zip files, Word documents, and so on - and the skin is using a generic icon to represent them, that icon can mysteriously vanish upon subsequent remakes of the album if some folders are excluded from processing.

For these reasons, the Process only updated subdirectories option is a dangerous one, unless you have a very clear understanding of how the album-building process works. The penalty for leaving it unchecked might be a bit of extra processing time, and the uploading of a few files that don't really need to be updated. But jAlbum won't generate new image files needlessly, and that's where the bulk of the processing and uploading time is.

This does not mean that you should force jAlbum to reprocess all of the images and videos by choosing Force Remake instead of Make Album. That's just a waste of processing and uploading time. But you should always let jAlbum process all of the subdirectories, whether they've been updated or not.