It stays put. Deactivating — or even deleting — the plugin leaves your chats, prompts, embeddings, vector index, and settings in the database, so reinstalling later picks up exactly where you left off. Nothing needs re-indexing after a temporary deactivation, and your API keys remain safely encrypted in the settings.
That durability cuts both ways: by default, removing the plugin does not scrub its data from your database. If you're retiring Wyregraf from a site for good, add this line to your site's wp-config.php before deleting the plugin:
define( 'WYREGRAF_REMOVE_ALL_DATA', true );
With that in place, deleting Wyregraf from the Plugins screen removes everything: chats, stored visitor conversations, embeddings and the vector index tables, prompts, namespaces, settings, and the saved API keys. Without it, deletion keeps the data for a future reinstall. Remember to take the line out of wp-config.php afterward.