@JsonFilter throws "JsonMappingException: Can not resolve BeanPropertyFilter"

I think you could trick the filtered writer defining an empty serialize filter for the cases where you want all the properties seralized:

FilterProvider filters = new SimpleFilterProvider().addFilter("apiFilter", SimpleBeanPropertyFilter.serializeAllExcept(emptySet));

This way, when the engine looks for the "apiFilter" filter defined at the @JsonFilter anotation, it finds it, but it will not have any effect (as will serialize all the properties).

EDIT Also, you can call the factory method writer() instead of filteredWriter():

ObjectWriter writer=null;
if(aplyFilter) {
    FilterProvider filters = new SimpleFilterProvider().addFilter("apiFilter", SimpleBeanPropertyFilter.filterOutAllExcept(filterProperties));
    writer=mapper.filteredWriter(filters);
} else {
   writer=mapper.writer();
}

return writer.writeValueAsString(user);

I think this last solution is way cleaner, and indeed better.

For Spring Boot / Jackson configuration just add:

@Configuration 
public class JacksonConfiguration { 
    public JacksonConfiguration(ObjectMapper objectMapper) { 
        objectMapper.setFilterProvider(new SimpleFilterProvider().setFailOnUnknownId(false)); 
    } 
}

I know it's already been answered but for any newcommers Jackson has actually added the ability to not fail on missing filters (JACKSON-650):
You just need to call SimpleFilterProvider.setFailOnUnknownId(false) and you won't get this exception.