In the Optimizer feature, some items offer different actions than others.
Login Items offer a Toggle button, while Launch Agents and Launch Daemons offer both a Toggle button but also a Checkbox to mark the item for deletion.
In macOS, the mechanics for Login Items are a bit different than Launch Agents/Daemons. Because of this, if you decide to disable a Login Item using the Toggle button, there is no record of it kept by macOS. Sensei will cache disabled items so that they can still be listed and re-enabled within the same session, but if Sensei is relaunched the cache will be reset and the list will only show the currently enabled Login Items.
If you need to re-enable a Login Item and it is not available in Sensei anymore, you need to go into the respective application and re-enable it. Most applications that enable Login Items expose a preference such as "Start the app on Login" that may need to be toggled Off and On for the Login Item to re-enable. Refer to the documentation of your app for how to enable its Login Item.