Table of Contents Knowledge base

Deactivating leaves your settings and every anchor alone.

Deleting removes them only if you ticked Delete everything when the plugin is deleted under Settings, which is off by default. On a network the tick is per site, and only the sites that asked are cleared.

Note that the anchors live in your posts' rendered output rather than in the posts themselves, so removing the plugin removes them — any link pointing at a #section on your site will stop resolving. Explicit ids you set by hand in the editor stay, because those are in the content.