Actually, uninstalling AL deleted everything in my Sims 2 folder, not just my downloads. It left two files that had foreign characters in them, though. So, a warning to anyone uninstalling AL -- backup your Sims2 directory.
Last time I uninstalled, which admittedly was years ago, the uninstall program asked me if I wanted to keep my saved games or not. Apparently answering "No" results in the removal of the entire The Sims 2 directory.
In any case backing up the directory is good practice when installing a new expansion pack or stuff pack. As a former network administrator, let me assure you that backups are ALWAYS good no matter how "unimportant" your data is.