In order to fix that, you can update ~/.emacs.d/.lsp-session-v1 to manually add the sub-directory.
> vi ~/.emacs.d/.lsp-session-v1 #s(lsp-session ("/Users/jerome/src/repo" "/Users/jerome/src/boss/sub-directory...
And then bounce Emacs.
Source: https://github.com/elixir-lsp/elixir-ls/issues/364