If facet values disappear after you select a value, it might be related to how you are passing the facet values.
When facet values are passed as elements of a string array, they are treated as OR (disjunctive). On the other hand, when facet values are passed as individual strings, they are treated as AND (conjunctive). For example, the following would find books written by Stephen King or belonging to the horror genre, while also being published by Penguin. You can find more on this here.
facetFilters: [["author:Stephen King", "genre:Horror"], "publisher:Penguin"]
If you are using conjunctive (AND) facet values, only the values that are present in records matching the selected facet value will remain available for further selection.