There is a limit imposed by the web server and as a consequence, the size of the set is limited. If you remove the old icons from the set fist and then try add the new ones it could work. Or create another set with the icons that do not fit in the first one. You can create links between sets by putting code like [ url=icon-set/folders]Go to the first part[/url] (without the space before url) in to the description field.
When you edit or create a new icon set, you can see all your icons that are not already in another set, so it is OK when you see the folders and adobe icons mixed.