If you install Searchanise in a store and clone this store's database to another store, the search results will be messed up. This is why we strongly recommend clean installations for new stores.
Searchanise identifies shops by unique API keys stored in the shops' database. When you clone a shop's database, you effectively create 2 Searchanise installations with the same API key, and the search results become mixed.
The proper way to resolve this issue is to uninstall Searchanise, delete database tables that store the API keys, and install Searchanise anew.
1. Uninstall Searchanise on the Add-ons → Manage add-ons page
2. Delete the cscart_se_settings database table
3. Install Searchanise on the Add-ons → Manage add-ons page
4. In the other Searchanise installation, click Force re-indexation