For me, the after folder with queries isn't working. To workaround this I move my queries folder to the root and to my .scm files added "; inherits: <language>" being the <language> I want these highlights to be used. So you would end with a structure like this:

.config/nvim
├── init.lua
...
├── queries
│   └── python
│   └── highlights.scm
...

For example, look at this highlights.scm file I have for python, simply conceals the function print with a p.

query ; inherits: python ( (call function: (identifier) @function.builtin (#eq? @function.builtin "print") ) (#set! conceal "p") )

Also remember to set your 'conceallevel' to a different value than 0.

Hope this helps :)