Before the very recent change (to use the new lsp API), .cquery_cached_index was put in the project root. Now it ends up in the directory containing the first file you edit, which is surely unintended (though will work OK if you have all source files in one directory).
(The problem is presumably cquery--get-init-params using default-directory. I can get my expected behaviour by setting cquery-cache-dir-function to a suitable find-project-root function.)