A core in Meilisearch is what holds your index. When changing core/index configuration such as synonyms, stop words, or protected words you need to reload the core to make the changes become active. To reload configuration you can either restart the whole Meilisearch server or simply reload a specific core. Here you can reload the site's cores/indexes.
This will simply empty the site's index. When doing so it will take care of only deleting the currently selected site's documents even if you index multiple sites into one index.
This will empty the Index Queue. It will take care of only deleting the currently selected site's Index Queue entries. You will have to re-initialize the Index Queue afterwards.