Try below filter to fetch the inactive users who has active application links
QueryOptions qo = new QueryOptions();
qo.addFilter(Filter.eq("inactive", true));
qo.addFilter(Filter.notnull("name"));
qo.addFilter(Filter.notnull("links.application.name"));
qo.addFilter(Filter.ne("links.application.name", ""));
qo.addFilter(Filter.ne("links.iiqDisabled",true));
For full code you can check below reference post