Good to hear you sorted that out @theshade! If I have time I might fix Pymakr to look in that folder on a raspi, although I think there are not many people running this setup. (ps Pymakr is open source, so if you want to do that yourself with a pull request, feel free)
For me this is the usual behavior of pymakr ide. The way I solve this is: push disconnect and restart from the host the WiFi connection. As soon as the WiFi connection is established, do a (re) connect and voila the RESP >>> prompt will appear.
With a Py board reset the WiFi state is not "in sync". Re-establishing the WiFi connection from the host forces this.
@jmarcelino In the board, I have a custom code running, and it shows what it should on the console, but whenever I try to upload a project, it fails. It had worked until I updated the plugin to the last version.