The autoload settings are stored in xml files named "PluginOptions.xml" in the "Documents\The Lord of the Rings Online\PluginData\accountName\serverName" folders where accountName is the name of your account and serverName is the name of the server you are logged on to.
Sometimes people will advise users to delete a specific .plugindata file and if the user can't find the specific file, they delete the entire folder thinking they will only lose stored settings. However, if you do anything like deleting the PluginData folder or perhaps the severName folder, then the client will create a new empty file the next time you log in and all of your autoload settings will be wiped out. If you didn't intentionally delete the folder, then something went wrong, perhaps the file got corrupted and couldn't be read in which case the client may have created a blank one in order to recover. Either way, unless you have a backup of the file, the autoload settings are gone and you will have to reset them.