Deactivating leaves your settings and every anchor alone. It asks your page cache to empty, so cached posts stop showing the list.
Deleting removes them only if you ticked Delete all data on uninstall under Settings, which is off by default. On a network the tick is per site, and only the sites that asked are cleared. With the tick on, deleting also takes out the sidebar widget, and a Contents (sidebar) or Table of Contents block you added under Appearance → Widgets when nothing else is in that widget.
If you switch the plugin off, or delete it without the tick, a block you added under Appearance → Widgets stays where it is and shows nothing. Some themes draw an empty box there. Remove the block under Appearance → Widgets if the plugin is not coming back.
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.
Still stuck? Ask the developers who wrote it. We aim to reply within one business day.
Table of Contents
Give a long post a contents list built from its own headings, and a permanent link to every section.
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